rs1560382

Variant names:

• chr2-7339206-T-C
• rs1560382

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 0.571 in 152,066 control chromosomes in the GnomAD database, including 25,443 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 0.57 (25443 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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: 0.571 AC: 86693 AN: 151948 Hom.: 25404 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.571 AC: 86790 AN: 152066 Hom.: 25443 Cov.: 33 AF XY: 0.571 AC XY: 42451 AN XY: 74362

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.581

Alfa AF: 0.467 Hom.: 2741

Bravo AF: 0.593

Asia WGS AF: 0.706 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.21
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1560382; hg19: chr2-7479337;