rs792718

Variant names:

• chr10-101159855-C-G
• rs792718
• ENST00000747668.1:n.331-7043C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-101159855-C-G
• chr10-101159855-C-T

Variant summary

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

The ENST00000747668.1(ENSG00000297387):​n.331-7043C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,100 control chromosomes in the GnomAD database, including 8,377 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 0.33 (8377 hom., cov: 32)
• Consequence: ENSG00000297387 ENST00000747668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 1 publications found

Genes affected

ENSG00000297387 (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 = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297387	ENST00000747668.1	n.331-7043C>G		intron_variant	Intron 1 of 1
ENSG00000297387	ENST00000747669.1	n.316-994C>G		intron_variant	Intron 1 of 3
ENSG00000297387	ENST00000747670.1	n.316-967C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49540 AN: 151982 Hom.: 8363 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.326 AC: 49590 AN: 152100 Hom.: 8377 Cov.: 32 AF XY: 0.325 AC XY: 24153 AN XY: 74364

African (AFR) AF: 0.396 AC: 16434 AN: 41488

American (AMR) AF: 0.262 AC: 3997 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 983 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1919 AN: 5170

South Asian (SAS) AF: 0.257 AC: 1236 AN: 4810

European-Finnish (FIN) AF: 0.330 AC: 3489 AN: 10584

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20482 AN: 67976

Other (OTH) AF: 0.326 AC: 689 AN: 2114

Alfa AF: 0.321 Hom.: 986

Bravo AF: 0.325

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.48
PhyloP100		-0.063

Splicing

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

Other links and lift over

dbSNP: rs792718; hg19: chr10-102919612;