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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791650.1. 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
	ENSG00000303087	ENST00000791650.1		n.51+6718C>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs754617;

hg19: chr10-44886342;