rs612353

Variant names:

• chr1-34647583-A-G
• rs612353
• ENST00000666642.1:n.569-6569T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000666642.1(ENSG00000287703):​n.569-6569T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,104 control chromosomes in the GnomAD database, including 15,466 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 0.45 (15466 hom., cov: 33)
• Consequence: ENSG00000287703 ENST00000666642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 2 publications found

Genes affected

ENSG00000287703 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666642.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287703	ENST00000666642.1		n.569-6569T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67990 AN: 151988 Hom.: 15436 Cov.: 33

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.448 AC: 68078 AN: 152104 Hom.: 15466 Cov.: 33 AF XY: 0.451 AC XY: 33560 AN XY: 74360

African (AFR) AF: 0.494 AC: 20480 AN: 41498

American (AMR) AF: 0.447 AC: 6834 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3470

East Asian (EAS) AF: 0.337 AC: 1737 AN: 5156

South Asian (SAS) AF: 0.509 AC: 2455 AN: 4824

European-Finnish (FIN) AF: 0.494 AC: 5218 AN: 10572

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28323 AN: 67986

Other (OTH) AF: 0.451 AC: 951 AN: 2110

Alfa AF: 0.429 Hom.: 23698

Bravo AF: 0.444

Asia WGS AF: 0.457 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.64
DANN	Benign	0.59
PhyloP100		-0.69

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs612353;

hg19: chr1-35113184;

COSMIC: COSV59937584;