rs1013344

Variant names:

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

Variant summary

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

The ENST00000606382.1(ENSG00000271955):​n.111-604G>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: ENSG00000271955 ENST00000606382.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

Genes affected

ENSG00000271955 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000271955	ENST00000606382.1	n.111-604G>A		intron_variant	Intron 1 of 3	5
ENSG00000271955	ENST00000650011.1	n.388-604G>A		intron_variant	Intron 3 of 5

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

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.552

Alfa AF: 0.566 Hom.: 24927

Bravo AF: 0.583

Asia WGS AF: 0.445 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1013344; hg19: chr2-60055010;