chr7-81781712-T-C

Variant names:

• chr7-81781712-T-C
• rs975360

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.372 in 151,952 control chromosomes in the GnomAD database, including 11,115 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 0.37 (11115 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 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

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56494 AN: 151834 Hom.: 11106 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.372 AC: 56530 AN: 151952 Hom.: 11115 Cov.: 31 AF XY: 0.372 AC XY: 27636 AN XY: 74250

African (AFR) AF: 0.308 AC: 12788 AN: 41472

American (AMR) AF: 0.303 AC: 4615 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1946 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1002 AN: 5154

South Asian (SAS) AF: 0.406 AC: 1956 AN: 4812

European-Finnish (FIN) AF: 0.427 AC: 4515 AN: 10562

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.418 AC: 28359 AN: 67922

Other (OTH) AF: 0.388 AC: 818 AN: 2110

Alfa AF: 0.402 Hom.: 23749

Bravo AF: 0.358

Asia WGS AF: 0.319 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	14
DANN	Benign	0.60
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs975360; hg19: chr7-81411028;