rs7848647

Variant names:

• chr9-114806766-T-C
• rs7848647

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 0.74 in 152,016 control chromosomes in the GnomAD database, including 42,427 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 0.74 (42427 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 59 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 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: 0.739 AC: 112320 AN: 151898 Hom.: 42373 Cov.: 31

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.740 AC: 112436 AN: 152016 Hom.: 42427 Cov.: 31 AF XY: 0.739 AC XY: 54924 AN XY: 74314

African (AFR) AF: 0.885 AC: 36736 AN: 41502

American (AMR) AF: 0.742 AC: 11333 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2646 AN: 3468

East Asian (EAS) AF: 0.508 AC: 2618 AN: 5154

South Asian (SAS) AF: 0.735 AC: 3534 AN: 4808

European-Finnish (FIN) AF: 0.697 AC: 7345 AN: 10532

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45935 AN: 67964

Other (OTH) AF: 0.720 AC: 1520 AN: 2110

Alfa AF: 0.704 Hom.: 105075

Bravo AF: 0.746

Asia WGS AF: 0.667 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-0.044

Splicing

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

Other links and lift over

dbSNP: rs7848647; hg19: chr9-117569046;