2-75041937-T-C

Position:

• chr2-75041937-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 0.477 in 152,128 control chromosomes in the GnomAD database, including 17,844 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 0.48 (17844 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 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: 0.477 AC: 72567 AN: 152010 Hom.: 17833 Cov.: 33

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.477 AC: 72616 AN: 152128 Hom.: 17844 Cov.: 33 AF XY: 0.471 AC XY: 35058 AN XY: 74386

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.492

Alfa AF: 0.461 Hom.: 22349

Bravo AF: 0.491

Asia WGS AF: 0.444 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.7
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: rs13012537; hg19: chr2-75269064;