7-106311063-C-T

Variant names:

• chr7-106311063-C-T
• rs997980

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.621

Alfa AF: 0.652 Hom.: 68459

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs997980; hg19: chr7-105951509;