chr10-20503405-G-A

Variant names:

• chr10-20503405-G-A
• rs7897194
• ENST00000785943.1:n.286-12284G>A

Variant summary

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

The ENST00000785943.1(ENSG00000302338):​n.286-12284G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,076 control chromosomes in the GnomAD database, including 2,747 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 (2747 hom., cov: 32)
• Consequence: ENSG00000302338 ENST00000785943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405
• Publications: 5 publications found

Genes affected

ENSG00000302338 (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 (AFR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785943.1. 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
	ENSG00000302338	ENST00000785943.1		n.286-12284G>A		intron	N/A
	ENSG00000302338	ENST00000785944.1		n.199-12284G>A		intron	N/A
	ENSG00000302338	ENST00000785945.1		n.133-12284G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26001 AN: 151958 Hom.: 2747 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.0253

Gnomad SAS AF: 0.0896

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.171 AC: 26025 AN: 152076 Hom.: 2747 Cov.: 32 AF XY: 0.170 AC XY: 12641 AN XY: 74334

African (AFR) AF: 0.293 AC: 12158 AN: 41464

American (AMR) AF: 0.127 AC: 1933 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0844 AC: 293 AN: 3470

East Asian (EAS) AF: 0.0254 AC: 131 AN: 5158

South Asian (SAS) AF: 0.0891 AC: 430 AN: 4828

European-Finnish (FIN) AF: 0.176 AC: 1858 AN: 10582

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.129 AC: 8757 AN: 67986

Other (OTH) AF: 0.133 AC: 281 AN: 2110

Alfa AF: 0.148 Hom.: 4061

Bravo AF: 0.173

Asia WGS AF: 0.0550 AC: 194 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.59
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs7897194; hg19: chr10-20792334;