rs856003

Variant names:

• chr10-117644052-G-A
• rs856003
• ENST00000806653.1:n.93-31449G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-117644052-G-A
• chr10-117644052-G-C
• chr10-117644052-G-T

Variant summary

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

The ENST00000806653.1(ENSG00000304858):​n.93-31449G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,118 control chromosomes in the GnomAD database, including 48,963 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 0.80 (48963 hom., cov: 33)
• Consequence: ENSG00000304858 ENST00000806653.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 0 publications found

Genes affected

ENSG00000304858 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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
ENSG00000304858	ENST00000806653.1	n.93-31449G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121746 AN: 152000 Hom.: 48947 Cov.: 33

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.801 AC: 121806 AN: 152118 Hom.: 48963 Cov.: 33 AF XY: 0.794 AC XY: 59066 AN XY: 74350

African (AFR) AF: 0.816 AC: 33856 AN: 41506

American (AMR) AF: 0.708 AC: 10826 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3035 AN: 3472

East Asian (EAS) AF: 0.811 AC: 4194 AN: 5174

South Asian (SAS) AF: 0.813 AC: 3925 AN: 4826

European-Finnish (FIN) AF: 0.743 AC: 7853 AN: 10564

Middle Eastern (MID) AF: 0.822 AC: 240 AN: 292

European-Non Finnish (NFE) AF: 0.814 AC: 55363 AN: 67982

Other (OTH) AF: 0.810 AC: 1710 AN: 2110

Alfa AF: 0.811 Hom.: 26188

Bravo AF: 0.799

Asia WGS AF: 0.757 AC: 2619 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.60
DANN	Benign	0.33
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs856003; hg19: chr10-119403563;