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. The variant received -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

Our verdict: Benign. The variant received -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 AFR exome AC: 0 AN: 0

Gnomad4 AMR exome AC: 0 AN: 0

Gnomad4 ASJ exome AC: 0 AN: 0

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 2

Gnomad4 SAS exome AC: 0 AN: 0

Gnomad4 FIN exome AF: 0.500 AC: 1 AN: 2

Gnomad4 NFE exome AF: 0.500 AC: 6 AN: 12

Gnomad4 Remaining exome AF: 0.500 AC: 1 AN: 2

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 AC: 0.356433 AN: 0.356433

Gnomad4 AMR AF: 0.660 AC: 0.659522 AN: 0.659522

Gnomad4 ASJ AF: 0.641 AC: 0.640589 AN: 0.640589

Gnomad4 EAS AF: 0.422 AC: 0.421796 AN: 0.421796

Gnomad4 SAS AF: 0.682 AC: 0.682138 AN: 0.682138

Gnomad4 FIN AF: 0.643 AC: 0.642789 AN: 0.642789

Gnomad4 NFE AF: 0.658 AC: 0.657583 AN: 0.657583

Gnomad4 OTH AF: 0.561 AC: 0.56108 AN: 0.56108

Alfa AF: 0.609 Hom.: 3884

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;