rs750160

Variant names:

• chr20-720987-T-C
• rs750160
• ENST00000840365.1:n.96-286T>C

Variant summary

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

The ENST00000840365.1(ENSG00000309339):​n.96-286T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,088 control chromosomes in the GnomAD database, including 9,687 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 0.32 (9687 hom., cov: 32)
• Consequence: ENSG00000309339 ENST00000840365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714
• Publications: 2 publications found

Genes affected

ENSG00000309339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 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
ENSG00000309339	ENST00000840365.1	n.96-286T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47928 AN: 151970 Hom.: 9666 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0253

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.316 AC: 47996 AN: 152088 Hom.: 9687 Cov.: 32 AF XY: 0.306 AC XY: 22728 AN XY: 74348

African (AFR) AF: 0.575 AC: 23848 AN: 41458

American (AMR) AF: 0.225 AC: 3433 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3468

East Asian (EAS) AF: 0.0258 AC: 133 AN: 5162

South Asian (SAS) AF: 0.129 AC: 621 AN: 4826

European-Finnish (FIN) AF: 0.178 AC: 1882 AN: 10580

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16387 AN: 67986

Other (OTH) AF: 0.315 AC: 665 AN: 2114

Alfa AF: 0.268 Hom.: 12992

Bravo AF: 0.332

Asia WGS AF: 0.136 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.49
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs750160; hg19: chr20-701631;