chr2-12824371-A-G

Position:

• chr2-12824371-A-G

Variant summary

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

The ENST00000663507.1(ENSG00000225649):​n.433-37391T>C 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 0.588 in 151,936 control chromosomes in the GnomAD database, including 26,627 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 0.59 (26627 hom., cov: 31)
• Consequence: ENST00000663507.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

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 (EAS) allele frequency at 95% confidence interval = 0.821 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
	ENST00000663507.1	n.433-37391T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89193 AN: 151818 Hom.: 26588 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.588 AC: 89286 AN: 151936 Hom.: 26627 Cov.: 31 AF XY: 0.589 AC XY: 43740 AN XY: 74236

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.572

Alfa AF: 0.565 Hom.: 17874

Bravo AF: 0.579

Asia WGS AF: 0.713 AC: 2480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10198628; hg19: chr2-12964497;