rs1031507

Variant names:

• chr2-191155892-A-C
• rs1031507
• ENST00000623836.1:n.179T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-191155892-A-C
• chr2-191155892-A-G

Variant summary

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

The ENST00000623836.1(ENSG00000280083):​n.179T>G 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 0.566 in 152,100 control chromosomes in the GnomAD database, including 25,972 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 0.57 (25970 hom., cov: 32)
  • Exomes 𝑓: 0.44 (2 hom.)
• Consequence: ENSG00000280083 ENST00000623836.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902

Genes affected

ENSG00000280083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.663 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
ENSG00000280083	ENST00000623836.1	n.179T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86086 AN: 151964 Hom.: 25953 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.564

GnomAD4 exome AF: 0.444 AC: 8 AN: 18 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 6 AN XY: 12

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.566 AC: 86148 AN: 152082 Hom.: 25970 Cov.: 32 AF XY: 0.572 AC XY: 42524 AN XY: 74358

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.561

Alfa AF: 0.621 Hom.: 3849

Bravo AF: 0.556

Asia WGS AF: 0.543 AC: 1885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1031507; hg19: chr2-192020618;