rs1013344

Variant names:

• chr2-59827875-C-T
• rs1013344
• ENST00000606382.1:n.111-604G>A

Variant summary

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

The ENST00000650011.1(ENSG00000233891):​n.388-604G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,804 control chromosomes in the GnomAD database, including 26,012 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 0.58 (26012 hom., cov: 32)
• Consequence: ENSG00000233891 ENST00000650011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 2 publications found

Genes affected

ENSG00000233891 (HGNC:58936):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650011.1. 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
	ENSG00000233891	ENST00000606382.1	TSL:5	n.111-604G>A		intron	N/A
	ENSG00000233891	ENST00000650011.1		n.388-604G>A		intron	N/A
	ENSG00000233891	ENST00000807304.1		n.115-604G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88120 AN: 151686 Hom.: 25967 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.581 AC: 88212 AN: 151804 Hom.: 26012 Cov.: 32 AF XY: 0.579 AC XY: 42963 AN XY: 74182

African (AFR) AF: 0.640 AC: 26492 AN: 41382

American (AMR) AF: 0.549 AC: 8376 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1828 AN: 3464

East Asian (EAS) AF: 0.393 AC: 2013 AN: 5122

South Asian (SAS) AF: 0.472 AC: 2268 AN: 4802

European-Finnish (FIN) AF: 0.614 AC: 6474 AN: 10552

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39012 AN: 67902

Other (OTH) AF: 0.552 AC: 1166 AN: 2112

Alfa AF: 0.571 Hom.: 32935

Bravo AF: 0.583

Asia WGS AF: 0.445 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.46
PhyloP100		-0.20

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: rs1013344;

hg19: chr2-60055010;