rs7853739

Variant names:

• chr9-100723537-A-C
• rs7853739

Your query was ambiguous. Multiple possible variants found:

• chr9-100723537-A-C
• chr9-100723537-A-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 0.262 in 151,968 control chromosomes in the GnomAD database, including 5,809 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 0.26 (5809 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 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: 0.262 AC: 39824 AN: 151848 Hom.: 5795 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.262 AC: 39872 AN: 151968 Hom.: 5809 Cov.: 31 AF XY: 0.264 AC XY: 19622 AN XY: 74290

African (AFR) AF: 0.359 AC: 14852 AN: 41408

American (AMR) AF: 0.378 AC: 5770 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 926 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1785 AN: 5150

South Asian (SAS) AF: 0.152 AC: 735 AN: 4822

European-Finnish (FIN) AF: 0.197 AC: 2086 AN: 10568

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12918 AN: 67978

Other (OTH) AF: 0.267 AC: 564 AN: 2112

Alfa AF: 0.214 Hom.: 17116

Bravo AF: 0.287

Asia WGS AF: 0.219 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs7853739; hg19: chr9-103485819;