rs7849556

Variant names:

• chr9-114720392-C-A
• rs7849556

Your query was ambiguous. Multiple possible variants found:

• chr9-114720392-C-A
• chr9-114720392-C-G
• chr9-114720392-C-T

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 0.779 in 152,082 control chromosomes in the GnomAD database, including 46,241 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 0.78 (46241 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 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: 0.779 AC: 118318 AN: 151966 Hom.: 46200 Cov.: 31

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.779 AC: 118412 AN: 152082 Hom.: 46241 Cov.: 31 AF XY: 0.783 AC XY: 58220 AN XY: 74348

African (AFR) AF: 0.803 AC: 33280 AN: 41454

American (AMR) AF: 0.771 AC: 11796 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2787 AN: 3468

East Asian (EAS) AF: 0.838 AC: 4330 AN: 5164

South Asian (SAS) AF: 0.838 AC: 4039 AN: 4818

European-Finnish (FIN) AF: 0.808 AC: 8573 AN: 10604

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.750 AC: 50996 AN: 67968

Other (OTH) AF: 0.776 AC: 1641 AN: 2114

Alfa AF: 0.724 Hom.: 5335

Bravo AF: 0.778

Asia WGS AF: 0.815 AC: 2836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.72
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs7849556; hg19: chr9-117482672; COSMIC: COSV60395492;