chr2-236684247-C-T

Position:

• chr2-236684247-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 0.0654 in 152,228 control chromosomes in the GnomAD database, including 397 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 0.065 (397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0717 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: 0.0654 AC: 9948 AN: 152110 Hom.: 397 Cov.: 32

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0430

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.00290

Gnomad SAS AF: 0.0276

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.0555

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

GnomAD4 genome AF: 0.0654 AC: 9950 AN: 152228 Hom.: 397 Cov.: 32 AF XY: 0.0672 AC XY: 5001 AN XY: 74428

Gnomad4 AFR AF: 0.0514

Gnomad4 AMR AF: 0.0428

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0280

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0734

Gnomad4 OTH AF: 0.0549

Alfa AF: 0.0745 Hom.: 55

Bravo AF: 0.0583

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2254387; hg19: chr2-237592890;