rs12639288

Positions:

• chr3-167943348-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651627.1(ENSG00000244706):​n.46-2993C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,844 control chromosomes in the GnomAD database, including 4,960 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 0.24 (4960 hom., cov: 31)
• Consequence: ENST00000651627.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651627.1	n.46-2993C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35978 AN: 151726 Hom.: 4960 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.237 AC: 35988 AN: 151844 Hom.: 4960 Cov.: 31 AF XY: 0.236 AC XY: 17481 AN XY: 74198

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.0509

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.237

Alfa AF: 0.285 Hom.: 6184

Bravo AF: 0.218

Asia WGS AF: 0.124 AC: 431 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12639288; hg19: chr3-167661136;