rs1343295

Variant names:

• chr1-166337516-T-C
• rs1343295
• ENST00000653824.3:n.359-1384T>C

Variant summary

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

The ENST00000653824.3(ENSG00000229588):​n.359-1384T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,024 control chromosomes in the GnomAD database, including 18,531 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 0.46 (18531 hom., cov: 32)
• Consequence: ENSG00000229588 ENST00000653824.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 4 publications found

Genes affected

ENSG00000229588 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653824.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229588	ENST00000653824.3		n.359-1384T>C		intron	N/A
	ENSG00000229588	ENST00000829274.1		n.179-1384T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69870 AN: 151906 Hom.: 18487 Cov.: 32

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.460 AC: 69979 AN: 152024 Hom.: 18531 Cov.: 32 AF XY: 0.464 AC XY: 34462 AN XY: 74314

African (AFR) AF: 0.715 AC: 29648 AN: 41456

American (AMR) AF: 0.471 AC: 7191 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3470

East Asian (EAS) AF: 0.704 AC: 3620 AN: 5144

South Asian (SAS) AF: 0.438 AC: 2117 AN: 4828

European-Finnish (FIN) AF: 0.334 AC: 3535 AN: 10570

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21547 AN: 67960

Other (OTH) AF: 0.453 AC: 956 AN: 2112

Alfa AF: 0.422 Hom.: 6231

Bravo AF: 0.486

Asia WGS AF: 0.574 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.77
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs1343295; hg19: chr1-166306753;