rs10491542

Variant names:

• chr9-82852387-G-A
• rs10491542
• ENST00000792604.1:n.266-21261C>T

Variant summary

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

The ENST00000792604.1(ENSG00000303186):​n.266-21261C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0805 in 152,092 control chromosomes in the GnomAD database, including 1,523 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 0.081 (1523 hom., cov: 32)
• Consequence: ENSG00000303186 ENST00000792604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 2 publications found

Genes affected

ENSG00000303186 (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 (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792604.1. 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
	ENSG00000303186	ENST00000792604.1		n.266-21261C>T		intron	N/A
	ENSG00000303186	ENST00000792605.1		n.113-21261C>T		intron	N/A
	ENSG00000303186	ENST00000792606.1		n.75-21261C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0804 AC: 12217 AN: 151974 Hom.: 1519 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0389

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.0423

Gnomad SAS AF: 0.00996

Gnomad FIN AF: 0.00989

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00241

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0805 AC: 12245 AN: 152092 Hom.: 1523 Cov.: 32 AF XY: 0.0779 AC XY: 5794 AN XY: 74356

African (AFR) AF: 0.265 AC: 10965 AN: 41428

American (AMR) AF: 0.0389 AC: 594 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00922 AC: 32 AN: 3470

East Asian (EAS) AF: 0.0418 AC: 216 AN: 5164

South Asian (SAS) AF: 0.00976 AC: 47 AN: 4816

European-Finnish (FIN) AF: 0.00989 AC: 105 AN: 10622

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00241 AC: 164 AN: 67992

Other (OTH) AF: 0.0535 AC: 113 AN: 2112

Alfa AF: 0.0264 Hom.: 1797

Bravo AF: 0.0930

Asia WGS AF: 0.0460 AC: 162 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	1.3
DANN	Benign	0.40
PhyloP100		-0.40

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: rs10491542;

hg19: chr9-85467302;