2-231418198-T-C

Variant names:

• chr2-231418198-T-C
• rs6750502

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 0.618 in 148,920 control chromosomes in the GnomAD database, including 29,901 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 0.62 (29901 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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: 0.618 AC: 91989 AN: 148824 Hom.: 29868 Cov.: 24

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.618 AC: 92068 AN: 148920 Hom.: 29901 Cov.: 24 AF XY: 0.624 AC XY: 45150 AN XY: 72408

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.608

Alfa AF: 0.540 Hom.: 38846

Bravo AF: 0.626

Asia WGS AF: 0.796 AC: 2770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6750502; hg19: chr2-232282909;