chr10-88003313-C-G

Variant names:

• chr10-88003313-C-G
• rs2142136
• ENST00000752269.1:n.191+10253C>G

Variant summary

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

The ENST00000752269.1(ENSG00000297977):​n.191+10253C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 151,944 control chromosomes in the GnomAD database, including 1,817 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 0.14 (1817 hom., cov: 32)
• Consequence: ENSG00000297977 ENST00000752269.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 7 publications found

Genes affected

ENSG00000297977 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752269.1. 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
	ENSG00000297977	ENST00000752269.1		n.191+10253C>G		intron	N/A
	ENSG00000297977	ENST00000752273.1		n.111+22506C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21178 AN: 151828 Hom.: 1808 Cov.: 32

Gnomad AFR AF: 0.0858

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.140 AC: 21209 AN: 151944 Hom.: 1817 Cov.: 32 AF XY: 0.140 AC XY: 10389 AN XY: 74246

African (AFR) AF: 0.0862 AC: 3570 AN: 41408

American (AMR) AF: 0.210 AC: 3208 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3466

East Asian (EAS) AF: 0.399 AC: 2070 AN: 5182

South Asian (SAS) AF: 0.128 AC: 614 AN: 4812

European-Finnish (FIN) AF: 0.108 AC: 1136 AN: 10558

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9763 AN: 67946

Other (OTH) AF: 0.148 AC: 312 AN: 2106

Alfa AF: 0.139 Hom.: 209

Bravo AF: 0.147

Asia WGS AF: 0.240 AC: 836 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.24
DANN	Benign	0.27
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2142136; hg19: chr10-89763070;