10-4108929-T-G

Variant names:

• chr10-4108929-T-G
• rs10795130
• ENST00000813037.1:n.144-6259A>C

Variant summary

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

The ENST00000813037.1(ENSG00000305807):​n.144-6259A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,162 control chromosomes in the GnomAD database, including 3,684 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 0.20 (3684 hom., cov: 32)
• Consequence: ENSG00000305807 ENST00000813037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• Publications: 6 publications found

Genes affected

ENSG00000305807 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813037.1. 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
	ENSG00000305807	ENST00000813037.1		n.144-6259A>C		intron	N/A
	ENSG00000305807	ENST00000813038.1		n.163-732A>C		intron	N/A
	ENSG00000305807	ENST00000813039.1		n.281-732A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29667 AN: 152042 Hom.: 3670 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.195 AC: 29719 AN: 152162 Hom.: 3684 Cov.: 32 AF XY: 0.192 AC XY: 14265 AN XY: 74404

African (AFR) AF: 0.351 AC: 14542 AN: 41476

American (AMR) AF: 0.159 AC: 2433 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3468

East Asian (EAS) AF: 0.112 AC: 580 AN: 5184

South Asian (SAS) AF: 0.180 AC: 869 AN: 4820

European-Finnish (FIN) AF: 0.0702 AC: 745 AN: 10608

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8866 AN: 67996

Other (OTH) AF: 0.196 AC: 414 AN: 2112

Alfa AF: 0.154 Hom.: 3498

Bravo AF: 0.207

Asia WGS AF: 0.169 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.31
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs10795130; hg19: chr10-4151121;