rs754617

Variant names:

• chr10-44390894-C-G
• rs754617
• ENST00000791650.1:n.51+6718C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-44390894-C-G
• chr10-44390894-C-T

Variant summary

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

The ENST00000791650.1(ENSG00000303087):​n.51+6718C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,118 control chromosomes in the GnomAD database, including 2,745 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 0.17 (2745 hom., cov: 32)
• Consequence: ENSG00000303087 ENST00000791650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 4 publications found

Genes affected

ENSG00000303087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984179	XR_001747298.2	n.67+1062C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303087	ENST00000791650.1	n.51+6718C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25289 AN: 152000 Hom.: 2744 Cov.: 32

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.166 AC: 25289 AN: 152118 Hom.: 2745 Cov.: 32 AF XY: 0.170 AC XY: 12619 AN XY: 74360

African (AFR) AF: 0.0420 AC: 1742 AN: 41522

American (AMR) AF: 0.321 AC: 4909 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3470

East Asian (EAS) AF: 0.135 AC: 694 AN: 5156

South Asian (SAS) AF: 0.106 AC: 511 AN: 4816

European-Finnish (FIN) AF: 0.232 AC: 2452 AN: 10568

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13729 AN: 67988

Other (OTH) AF: 0.204 AC: 430 AN: 2112

Alfa AF: 0.0632 Hom.: 87

Bravo AF: 0.171

Asia WGS AF: 0.117 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.43
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs754617; hg19: chr10-44886342;