rs2608077

chr3-142914604-G-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, non coding transcript 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: ENST00000658594.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

Genes affected

(HGNC:):

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658594.1	n.195+2294G>A		intron_variant, non_coding_transcript_variant
	ENST00000663511.1	n.169+2294G>A		intron_variant, non_coding_transcript_variant

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;