rs7088285

Variant names:

• chr10-44392481-G-A
• rs7088285
• ENST00000791650.1:n.52-5676G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-44392481-G-A
• chr10-44392481-G-C
• chr10-44392481-G-T

Variant summary

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

The ENST00000791650.1(ENSG00000303087):​n.52-5676G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,324 control chromosomes in the GnomAD database, including 3,456 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 0.20 (3456 hom., cov: 31)
• Consequence: ENSG00000303087 ENST00000791650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 7 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 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.52-5676G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30550 AN: 151208 Hom.: 3446 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.202 AC: 30581 AN: 151324 Hom.: 3456 Cov.: 31 AF XY: 0.204 AC XY: 15044 AN XY: 73900

African (AFR) AF: 0.130 AC: 5364 AN: 41166

American (AMR) AF: 0.209 AC: 3180 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 928 AN: 3456

East Asian (EAS) AF: 0.432 AC: 2216 AN: 5130

South Asian (SAS) AF: 0.279 AC: 1323 AN: 4750

European-Finnish (FIN) AF: 0.201 AC: 2106 AN: 10468

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14677 AN: 67846

Other (OTH) AF: 0.237 AC: 495 AN: 2090

Alfa AF: 0.139 Hom.: 395

Bravo AF: 0.198

Asia WGS AF: 0.361 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.60
PhyloP100		-3.0

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: rs7088285;

hg19: chr10-44887929;