chr7-85982167-G-T

Variant names:

• chr7-85982167-G-T
• rs10245061
• ENST00000757672.1:n.224-15566C>A

Variant summary

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

The ENST00000757672.1(ENSG00000298738):​n.224-15566C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,862 control chromosomes in the GnomAD database, including 27,308 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 (27308 hom., cov: 31)
• Consequence: ENSG00000298738 ENST00000757672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572
• Publications: 6 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=-1.03).
• 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.224-15566C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87049 AN: 151744 Hom.: 27252 Cov.: 31

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.574 AC: 87160 AN: 151862 Hom.: 27308 Cov.: 31 AF XY: 0.567 AC XY: 42098 AN XY: 74242

African (AFR) AF: 0.841 AC: 34869 AN: 41472

American (AMR) AF: 0.475 AC: 7229 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1780 AN: 3466

East Asian (EAS) AF: 0.357 AC: 1844 AN: 5162

South Asian (SAS) AF: 0.376 AC: 1813 AN: 4820

European-Finnish (FIN) AF: 0.498 AC: 5237 AN: 10518

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

European-Non Finnish (NFE) AF: 0.477 AC: 32368 AN: 67886

Other (OTH) AF: 0.559 AC: 1180 AN: 2110

Alfa AF: 0.497 Hom.: 32631

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	-1.0
CADD	Benign	8.1
DANN	Benign	0.57
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs10245061; hg19: chr7-85611483;