rs994247

chr7-8760938-C-T

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 0.0874 in 151,992 control chromosomes in the GnomAD database, including 665 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 0.087 (665 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0873 AC: 13262 AN: 151876 Hom.: 664 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0736

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.0874 AC: 13279 AN: 151992 Hom.: 665 Cov.: 32 AF XY: 0.0868 AC XY: 6449 AN XY: 74278

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0772

Gnomad4 ASJ AF: 0.0594

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0316

Gnomad4 NFE AF: 0.0736

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0769 Hom.: 380

Bravo AF: 0.0887

Asia WGS AF: 0.145 AC: 504 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	0.30
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs994247; hg19: chr7-8800568;