dbSNP rs17501108: ENSG00000300407:n.118-5645G>T (chr7-81774578-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000771413.1(ENSG00000300407):n.118-5645G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,062 control chromosomes in the GnomAD database, including 907 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 0.11 ( 907 hom., cov: 32)

Consequence

ENSG00000300407
ENST00000771413.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.434

Publications

14 publications found

Variant links:

Genes affected

ENSG00000300407 (HGNC:):

ENSG00000300407 links:

Genome browser will be placed here

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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300407	ENST00000771413.1 link	n.118-5645G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16333

AN:

151944

Hom.:

904

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.0773

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.00964

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.0867

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.108

AC:

16354

AN:

152062

Hom.:

907

Cov.:

AF XY:

0.108

AC XY:

7997

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.113

AC:

4671

AN:

41476

American (AMR)

AF:

0.0772

AC:

1179

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

398

AN:

3472

East Asian (EAS)

AF:

0.00966

AC:

AN:

5174

South Asian (SAS)

AF:

0.104

AC:

500

AN:

4826

European-Finnish (FIN)

AF:

0.143

AC:

1506

AN:

10566

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.113

AC:

7663

AN:

67966

Other (OTH)

AF:

0.0858

AC:

181

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

739

1479

2218

2958

3697

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<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:

0.105

Hom.:

349

Bravo

AF:

0.101

Asia WGS

AF:

0.0700

AC:

247

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.39

(source)

DANN

Benign

0.58

PhyloP100

-0.43

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