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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.267

Alfa AF: 0.201 Hom.: 6858

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7853739; hg19: chr9-103485819;