dbSNP rs1043274: CYB561D1:c.*3563C>T (chr1-109499822-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_182580.3(CYB561D1):c.*3563C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0962 in 152,294 control chromosomes in the GnomAD database, including 2,342 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.096 ( 2342 hom., cov: 32)

Exomes 𝑓: 0.016 ( 0 hom. )

Consequence

CYB561D1
NM_182580.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.833

Publications

6 publications found

Variant links:

Genes affected

CYB561D1 (HGNC:26804): (cytochrome b561 family member D1) Predicted to enable heme binding activity and oxidoreductase activity. Predicted to be involved in transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

CYB561D1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYB561D1	NM_182580.3 link	c.*3563C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000420578.7	NP_872386.1	Q8N8Q1-1Q6ZQS1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CYB561D1	ENST00000420578.7 link	c.*3563C>T	3_prime_UTR_variant	Exon 3 of 3	1	NM_182580.3	ENSP00000413530.2	Q8N8Q1-1
CYB561D1	ENST00000310611.8 link	c.*3955C>T	3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000309324.4	Q8N8Q1-2
CYB561D1	ENST00000430195.2 link	c.*4047C>T	3_prime_UTR_variant	Exon 4 of 4	2		ENSP00000416898.2	Q8N8Q1-4
CYB561D1	ENST00000528785.1 link	c.687-2561C>T	intron_variant	Intron 3 of 3	5		ENSP00000434344.1	E9PQU0

Frequencies

GnomAD3 genomes

AF:

0.0960

AC:

14603

AN:

152114

Hom.:

2329

Cov.:

show subpopulations

Gnomad AFR

AF:

0.329

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0339

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0435

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00159

Gnomad OTH

AF:

0.0621

GnomAD4 exome

AF:

0.0161

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0238

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0227

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0962

AC:

14644

AN:

152232

Hom.:

2342

Cov.:

AF XY:

0.0936

AC XY:

6968

AN XY:

74448

show subpopulations

African (AFR)

AF:

0.329

AC:

13651

AN:

41484

American (AMR)

AF:

0.0338

AC:

517

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.00519

AC:

AN:

3468

East Asian (EAS)

AF:

0.00135

AC:

AN:

5180

South Asian (SAS)

AF:

0.0433

AC:

209

AN:

4828

European-Finnish (FIN)

AF:

0.0000942

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00159

AC:

108

AN:

68028

Other (OTH)

AF:

0.0615

AC:

130

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

501

1002

1504

2005

2506

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

264

396

528

660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0360

Hom.:

942

Bravo

AF:

0.108

Asia WGS

AF:

0.0460

AC:

162

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.62

PhyloP100

0.83

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over