rs10498902

Variant names:

• chr6-74768915-G-A
• rs10498902
• ENST00000740411.1:n.89+37474C>T

Variant summary

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

The ENST00000740411.1(ENSG00000272243):​n.89+37474C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 152,274 control chromosomes in the GnomAD database, including 102 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 0.014 (102 hom., cov: 32)
• Consequence: ENSG00000272243 ENST00000740411.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452
• Publications: 0 publications found

Genes affected

ENSG00000272243 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740411.1. 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
	ENSG00000272243	ENST00000740411.1		n.89+37474C>T		intron	N/A
	ENSG00000272243	ENST00000740412.1		n.44+37474C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0139 AC: 2112 AN: 152156 Hom.: 102 Cov.: 32

Gnomad AFR AF: 0.00125

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.00499

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00482

Gnomad OTH AF: 0.0191

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

GnomAD4 genome AF: 0.0138 AC: 2108 AN: 152274 Hom.: 102 Cov.: 32 AF XY: 0.0166 AC XY: 1237 AN XY: 74450

African (AFR) AF: 0.00125 AC: 52 AN: 41576

American (AMR) AF: 0.0364 AC: 557 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3472

East Asian (EAS) AF: 0.136 AC: 703 AN: 5176

South Asian (SAS) AF: 0.0740 AC: 356 AN: 4812

European-Finnish (FIN) AF: 0.00499 AC: 53 AN: 10618

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00482 AC: 328 AN: 68004

Other (OTH) AF: 0.0194 AC: 41 AN: 2116

Alfa AF: 0.00731 Hom.: 11

Bravo AF: 0.0145

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.19
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs10498902; hg19: chr6-75478631;