2-67412637-G-T

Position:

• chr2-67412637-G-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 0.737 in 151,958 control chromosomes in the GnomAD database, including 41,686 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 0.74 (41686 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.918

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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: 0.737 AC: 111927 AN: 151840 Hom.: 41662 Cov.: 31

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.737 AC: 112008 AN: 151958 Hom.: 41686 Cov.: 31 AF XY: 0.732 AC XY: 54367 AN XY: 74268

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.767

Alfa AF: 0.721 Hom.: 52024

Bravo AF: 0.745

Asia WGS AF: 0.698 AC: 2428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1486134; hg19: chr2-67639769;