rs1043274

chr1-109499822-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.833

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CYB561D1	NM_182580.3	c.*3563C>T		3_prime_UTR_variant	3/3	ENST00000420578.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYB561D1	ENST00000420578.7	c.*3563C>T		3_prime_UTR_variant	3/3	1	NM_182580.3	P4
CYB561D1	ENST00000310611.8	c.*3955C>T		3_prime_UTR_variant	4/4	1
CYB561D1	ENST00000430195.2	c.*4047C>T		3_prime_UTR_variant	4/4	2
CYB561D1	ENST00000528785.1	c.687-2561C>T		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14603 AN: 152114 Hom.: 2329 Cov.: 32

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: 1 AN: 62 Hom.: 0 Cov.: 0 AF XY: 0.0238 AC XY: 1 AN XY: 42

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0227

GnomAD4 genome AF: 0.0962 AC: 14644 AN: 152232 Hom.: 2342 Cov.: 32 AF XY: 0.0936 AC XY: 6968 AN XY: 74448

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.0338

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0433

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00159

Gnomad4 OTH AF: 0.0615

Alfa AF: 0.0223 Hom.: 362

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	13
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1043274; hg19: chr1-110042444;