chr2-239496966-G-A

Position:

• chr2-239496966-G-A

Variant summary

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

The ENST00000659636.1(ENSG00000286525):​n.318-32660G>A 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 0.165 in 150,812 control chromosomes in the GnomAD database, including 2,207 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 0.16 (2207 hom., cov: 33)
• Consequence: ENST00000659636.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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
	ENST00000659636.1	n.318-32660G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.165 AC: 24833 AN: 150692 Hom.: 2207 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.00743

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.165 AC: 24847 AN: 150812 Hom.: 2207 Cov.: 33 AF XY: 0.162 AC XY: 11912 AN XY: 73562

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.00745

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.159

Alfa AF: 0.151 Hom.: 4163

Bravo AF: 0.160

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6743931; hg19: chr2-240418660;