7-85982309-A-G

Variant names:

• chr7-85982309-A-G
• rs10274362
• ENST00000757672.1:n.224-15708T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000757672.1(ENSG00000298738):​n.224-15708T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,716 control chromosomes in the GnomAD database, including 27,256 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 0.57 (27256 hom., cov: 30)
• Consequence: ENSG00000298738 ENST00000757672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 5 publications found

Genes affected

ENSG00000298738 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 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
ENSG00000298738	ENST00000757672.1	n.224-15708T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86883 AN: 151596 Hom.: 27199 Cov.: 30

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.573 AC: 86996 AN: 151716 Hom.: 27256 Cov.: 30 AF XY: 0.566 AC XY: 42003 AN XY: 74146

African (AFR) AF: 0.841 AC: 34807 AN: 41406

American (AMR) AF: 0.474 AC: 7193 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1779 AN: 3464

East Asian (EAS) AF: 0.357 AC: 1839 AN: 5150

South Asian (SAS) AF: 0.375 AC: 1806 AN: 4814

European-Finnish (FIN) AF: 0.496 AC: 5222 AN: 10530

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32333 AN: 67862

Other (OTH) AF: 0.558 AC: 1175 AN: 2106

Alfa AF: 0.491 Hom.: 7625

Bravo AF: 0.588

Asia WGS AF: 0.418 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.36
DANN	Benign	0.38
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10274362; hg19: chr7-85611625;