rs2892976

Variant names:

• chr13-99406307-G-A
• rs2892976
• ENST00000642991.1:n.2921C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-99406307-G-A
• chr13-99406307-G-C

Variant summary

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

The ENST00000642991.1(ENSG00000290577):​n.2921C>T 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 0.713 in 152,158 control chromosomes in the GnomAD database, including 39,548 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 0.71 (39537 hom., cov: 32)
  • Exomes 𝑓: 0.84 (11 hom.)
• Consequence: ENSG00000290577 ENST00000642991.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 14 publications found

Genes affected

ENSG00000290577 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642991.1. 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
	ENSG00000290577	ENST00000642991.1		n.2921C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108431 AN: 152008 Hom.: 39524 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.708

GnomAD4 exome AF: 0.844 AC: 27 AN: 32 Hom.: 11 Cov.: 0 AF XY: 0.833 AC XY: 20 AN XY: 24

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.750 AC: 9 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.857 AC: 12 AN: 14

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.713 AC: 108481 AN: 152126 Hom.: 39537 Cov.: 32 AF XY: 0.711 AC XY: 52910 AN XY: 74392

African (AFR) AF: 0.566 AC: 23486 AN: 41470

American (AMR) AF: 0.694 AC: 10613 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2347 AN: 3470

East Asian (EAS) AF: 0.648 AC: 3358 AN: 5184

South Asian (SAS) AF: 0.704 AC: 3393 AN: 4820

European-Finnish (FIN) AF: 0.747 AC: 7903 AN: 10584

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54822 AN: 67992

Other (OTH) AF: 0.707 AC: 1491 AN: 2110

Alfa AF: 0.783 Hom.: 118479

Bravo AF: 0.703

Asia WGS AF: 0.627 AC: 2183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.62
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2892976; hg19: chr13-100058561;