7-106311063-C-T

Variant names:

• chr7-106311063-C-T
• rs997980

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 0.593 in 151,908 control chromosomes in the GnomAD database, including 27,845 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 0.59 (27845 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.737 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: 0.593 AC: 90034 AN: 151790 Hom.: 27849 Cov.: 30

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.593 AC: 90050 AN: 151908 Hom.: 27845 Cov.: 30 AF XY: 0.592 AC XY: 43987 AN XY: 74242

African (AFR) AF: 0.422 AC: 17494 AN: 41416

American (AMR) AF: 0.628 AC: 9595 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2142 AN: 3466

East Asian (EAS) AF: 0.399 AC: 2055 AN: 5146

South Asian (SAS) AF: 0.758 AC: 3646 AN: 4810

European-Finnish (FIN) AF: 0.640 AC: 6755 AN: 10554

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46347 AN: 67932

Other (OTH) AF: 0.621 AC: 1311 AN: 2110

Alfa AF: 0.643 Hom.: 130594

Bravo AF: 0.574

Asia WGS AF: 0.603 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.068
DANN	Benign	0.50
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs997980; hg19: chr7-105951509;