rs10021692

Variant names:

• chr4-187159831-G-A
• rs10021692
• ENST00000782343.1:n.2001G>A

Variant summary

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

The ENST00000782343.1(ENSG00000301857):​n.2001G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,110 control chromosomes in the GnomAD database, including 1,209 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 0.12 (1209 hom., cov: 32)
• Consequence: ENSG00000301857 ENST00000782343.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 4 publications found

Genes affected

ENSG00000301857 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.151 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
ENSG00000301857	ENST00000782343.1	n.2001G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18621 AN: 151992 Hom.: 1206 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0746

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.122 AC: 18633 AN: 152110 Hom.: 1209 Cov.: 32 AF XY: 0.126 AC XY: 9371 AN XY: 74350

African (AFR) AF: 0.131 AC: 5433 AN: 41474

American (AMR) AF: 0.156 AC: 2385 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 470 AN: 3470

East Asian (EAS) AF: 0.0742 AC: 384 AN: 5178

South Asian (SAS) AF: 0.121 AC: 584 AN: 4828

European-Finnish (FIN) AF: 0.171 AC: 1810 AN: 10558

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7260 AN: 68016

Other (OTH) AF: 0.103 AC: 217 AN: 2104

Alfa AF: 0.110 Hom.: 1558

Bravo AF: 0.119

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.39
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs10021692; hg19: chr4-188080985;