rs2608077

Variant names:

• chr3-142914604-G-A
• rs2608077
• ENST00000658594.1:n.195+2294G>A

Variant summary

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

The ENST00000658594.1(ENSG00000243818):​n.195+2294G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,986 control chromosomes in the GnomAD database, including 10,192 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 0.35 (10192 hom., cov: 32)
• Consequence: ENSG00000243818 ENST00000658594.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

Genes affected

ENSG00000243818 (HGNC:56713):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243818	ENST00000658594.1	n.195+2294G>A		intron_variant	Intron 1 of 2
ENSG00000243818	ENST00000663511.1	n.169+2294G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53518 AN: 151868 Hom.: 10180 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.352 AC: 53566 AN: 151986 Hom.: 10192 Cov.: 32 AF XY: 0.353 AC XY: 26208 AN XY: 74292

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.346

Alfa AF: 0.294 Hom.: 2790

Bravo AF: 0.363

Asia WGS AF: 0.357 AC: 1241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2608077; hg19: chr3-142633446;