7-91910403-C-T

Variant names:

• chr7-91910403-C-T
• rs7781767

Variant summary

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

The variant allele was found at a frequency of 0.195 in 151,948 control chromosomes in the GnomAD database, including 4,080 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 0.19 (4080 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 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: 0.195 AC: 29553 AN: 151828 Hom.: 4072 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0952

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.195 AC: 29582 AN: 151948 Hom.: 4080 Cov.: 31 AF XY: 0.196 AC XY: 14520 AN XY: 74248

African (AFR) AF: 0.379 AC: 15686 AN: 41420

American (AMR) AF: 0.132 AC: 2011 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3472

East Asian (EAS) AF: 0.390 AC: 2004 AN: 5138

South Asian (SAS) AF: 0.183 AC: 882 AN: 4812

European-Finnish (FIN) AF: 0.0952 AC: 1005 AN: 10562

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7111 AN: 67960

Other (OTH) AF: 0.171 AC: 360 AN: 2108

Alfa AF: 0.133 Hom.: 5684

Bravo AF: 0.206

Asia WGS AF: 0.253 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7781767; hg19: chr7-91539717;