rs10499889

Variant names:

• chr7-85491748-T-C
• rs10499889
• ENST00000795228.1:n.64-17321A>G

Variant summary

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

The ENST00000795228.1(ENSG00000303520):​n.64-17321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,626 control chromosomes in the GnomAD database, including 10,066 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 0.35 (10066 hom., cov: 31)
• Consequence: ENSG00000303520 ENST00000795228.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 5 publications found

Genes affected

ENSG00000303520 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795228.1. 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
	ENSG00000303520	ENST00000795228.1		n.64-17321A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52795 AN: 151508 Hom.: 10069 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.0326

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.348 AC: 52789 AN: 151626 Hom.: 10066 Cov.: 31 AF XY: 0.342 AC XY: 25370 AN XY: 74084

African (AFR) AF: 0.262 AC: 10836 AN: 41428

American (AMR) AF: 0.286 AC: 4345 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1213 AN: 3460

East Asian (EAS) AF: 0.0327 AC: 169 AN: 5174

South Asian (SAS) AF: 0.381 AC: 1833 AN: 4810

European-Finnish (FIN) AF: 0.400 AC: 4216 AN: 10544

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.425 AC: 28790 AN: 67710

Other (OTH) AF: 0.365 AC: 768 AN: 2102

Alfa AF: 0.386 Hom.: 11929

Bravo AF: 0.335

Asia WGS AF: 0.200 AC: 699 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.65
PhyloP100		0.53

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: rs10499889;

hg19: chr7-85121064;