chr2-41046491-T-C

Position:

• chr2-41046491-T-C

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 0.068 in 152,222 control chromosomes in the GnomAD database, including 663 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 0.068 (663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10348 AN: 152104 Hom.: 659 Cov.: 32

Gnomad AFR AF: 0.0142

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0735

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0680 AC: 10354 AN: 152222 Hom.: 663 Cov.: 32 AF XY: 0.0708 AC XY: 5269 AN XY: 74420

Gnomad4 AFR AF: 0.0142

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0735

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.0652

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0692 Hom.: 374

Bravo AF: 0.0697

Asia WGS AF: 0.214 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17027130; hg19: chr2-41273631;