rs2724041

Variant names:

• chr7-96447615-G-A
• rs2724041

Your query was ambiguous. Multiple possible variants found:

• chr7-96447615-G-A
• chr7-96447615-G-C
• chr7-96447615-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.642 in 152,006 control chromosomes in the GnomAD database, including 32,207 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 0.64 (32207 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.67

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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: 0.642 AC: 97457 AN: 151888 Hom.: 32159 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.642 AC: 97562 AN: 152006 Hom.: 32207 Cov.: 32 AF XY: 0.642 AC XY: 47715 AN XY: 74282

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.680

Alfa AF: 0.577 Hom.: 51915

Bravo AF: 0.660

Asia WGS AF: 0.774 AC: 2689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2724041; hg19: chr7-96076927;