rs556648

Variant names:

• chr1-214947253-G-A
• rs556648
• ENST00000658732.1:n.345G>A

Variant summary

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

The ENST00000658732.1(ENSG00000287008):​n.345G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,038 control chromosomes in the GnomAD database, including 15,807 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 0.39 (15807 hom., cov: 32)
• Consequence: ENSG00000287008 ENST00000658732.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

Genes affected

ENSG00000287008 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 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
ENSG00000287008	ENST00000658732.1	n.345G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59046 AN: 151916 Hom.: 15759 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.389 AC: 59152 AN: 152038 Hom.: 15807 Cov.: 32 AF XY: 0.385 AC XY: 28580 AN XY: 74314

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.359

Alfa AF: 0.332 Hom.: 1509

Bravo AF: 0.410

Asia WGS AF: 0.393 AC: 1358 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.92
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs556648; hg19: chr1-215120596; COSMIC: COSV71980335;