rs6430612

chr2-136248628-C-T

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 0.43 in 151,898 control chromosomes in the GnomAD database, including 16,452 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 0.43 (16452 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) 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: 0.430 AC: 65237 AN: 151780 Hom.: 16455 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.430 AC: 65249 AN: 151898 Hom.: 16452 Cov.: 31 AF XY: 0.419 AC XY: 31116 AN XY: 74240

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.0528

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.316

Alfa AF: 0.487 Hom.: 30025

Bravo AF: 0.397

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	0.17
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6430612; hg19: chr2-137006198;