2-41298982-T-C

Variant names:

• chr2-41298982-T-C
• rs1508116

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 0.809 in 152,152 control chromosomes in the GnomAD database, including 50,115 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 0.81 (50115 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 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: 0.809 AC: 122922 AN: 152034 Hom.: 50066 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.809 AC: 123028 AN: 152152 Hom.: 50115 Cov.: 31 AF XY: 0.812 AC XY: 60381 AN XY: 74352

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.807

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.790

Alfa AF: 0.795 Hom.: 5977

Bravo AF: 0.812

Asia WGS AF: 0.867 AC: 3015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1508116; hg19: chr2-41526122;