rs7947387

Positions:

• chr11-38924616-G-A
• chr11-38924616-G-C

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 0.039 in 151,814 control chromosomes in the GnomAD database, including 168 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 0.039 (168 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.38924616G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0390 AC: 5921 AN: 151696 Hom.: 169 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.0736

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0144

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0390 AC: 5914 AN: 151814 Hom.: 168 Cov.: 32 AF XY: 0.0370 AC XY: 2744 AN XY: 74200

Gnomad4 AFR AF: 0.0117

Gnomad4 AMR AF: 0.0391

Gnomad4 ASJ AF: 0.0736

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.0140

Gnomad4 FIN AF: 0.0225

Gnomad4 NFE AF: 0.0597

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0187 Hom.: 7

Bravo AF: 0.0400

Asia WGS AF: 0.00751 AC: 26 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.77
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7947387; hg19: chr11-38946166;