rs6947787

Variant names:

• chr7-140263596-A-G
• rs6947787

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 0.165 in 152,142 control chromosomes in the GnomAD database, including 3,037 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 0.17 (3037 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 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: 0.165 AC: 25066 AN: 152024 Hom.: 3029 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.0773

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.165 AC: 25105 AN: 152142 Hom.: 3037 Cov.: 32 AF XY: 0.162 AC XY: 12085 AN XY: 74400

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.0996

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.0771

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0899

Gnomad4 OTH AF: 0.155

Alfa AF: 0.105 Hom.: 937

Bravo AF: 0.170

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6947787; hg19: chr7-139963396;