rs4672507

chr2-62343438-T-Achr2-62343438-T-Cchr2-62343438-T-G

Variant summary

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

The ENST00000689590.1(ENSG00000228541):n.163+46992T>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 0.598 in 152,020 control chromosomes in the GnomAD database, including 27,316 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 0.60 (27316 hom., cov: 32)
• Consequence: ENST00000689590.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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 (SAS) allele frequency at 95% confidence interval = 0.657 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
	ENST00000689590.1	n.163+46992T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90839 AN: 151900 Hom.: 27282 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.598 AC: 90938 AN: 152020 Hom.: 27316 Cov.: 32 AF XY: 0.600 AC XY: 44590 AN XY: 74282

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.583

Alfa AF: 0.612 Hom.: 3387

Bravo AF: 0.590

Asia WGS AF: 0.633 AC: 2203 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	1.8
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4672507; hg19: chr2-62570573;