rs2760496

Variant names:

• chr1-58776356-A-C
• rs2760496

Your query was ambiguous. Multiple possible variants found:

• chr1-58776356-A-C
• chr1-58776356-A-G
• chr1-58776356-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 0.264 in 151,912 control chromosomes in the GnomAD database, including 5,922 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 (5922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.492 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: 0.264 AC: 40015 AN: 151794 Hom.: 5912 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.264 AC: 40059 AN: 151912 Hom.: 5922 Cov.: 32 AF XY: 0.276 AC XY: 20461 AN XY: 74222

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.285

Alfa AF: 0.267 Hom.: 5621

Bravo AF: 0.253

Asia WGS AF: 0.488 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.080
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2760496; hg19: chr1-59242028;