rs1023102

Variant names:

• chr13-73250879-A-G
• rs1023102
• ENST00000755971.1:n.172-246A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-73250879-A-G
• chr13-73250879-A-T

Variant summary

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

The ENST00000755971.1(ENSG00000298494):​n.172-246A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,938 control chromosomes in the GnomAD database, including 17,279 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 0.47 (17279 hom., cov: 31)
• Consequence: ENSG00000298494 ENST00000755971.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 4 publications found

Genes affected

ENSG00000298494 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755971.1. 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
	ENSG00000298494	ENST00000755971.1		n.172-246A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71949 AN: 151820 Hom.: 17258 Cov.: 31

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.474 AC: 72008 AN: 151938 Hom.: 17279 Cov.: 31 AF XY: 0.476 AC XY: 35311 AN XY: 74250

African (AFR) AF: 0.466 AC: 19310 AN: 41446

American (AMR) AF: 0.550 AC: 8388 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3470

East Asian (EAS) AF: 0.588 AC: 3033 AN: 5160

South Asian (SAS) AF: 0.597 AC: 2870 AN: 4810

European-Finnish (FIN) AF: 0.398 AC: 4204 AN: 10552

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31042 AN: 67928

Other (OTH) AF: 0.479 AC: 1011 AN: 2112

Alfa AF: 0.466 Hom.: 11254

Bravo AF: 0.485

Asia WGS AF: 0.612 AC: 2132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.3
DANN	Benign	0.78
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1023102; hg19: chr13-73825016;