rs1543400

Variant names:

• chr20-40833953-C-G
• rs1543400
• ENST00000758964.1:n.86+32148G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000758964.1(ENSG00000229771):​n.86+32148G>C variant causes a intron change. The variant allele was found at a frequency of 0.432 in 152,066 control chromosomes in the GnomAD database, including 14,651 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 0.43 (14651 hom., cov: 33)
• Consequence: ENSG00000229771 ENST00000758964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.66
• Publications: 1 publications found

Genes affected

ENSG00000229771 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 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
ENSG00000229771	ENST00000758964.1	n.86+32148G>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65558 AN: 151946 Hom.: 14633 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.432 AC: 65621 AN: 152066 Hom.: 14651 Cov.: 33 AF XY: 0.429 AC XY: 31899 AN XY: 74308

African (AFR) AF: 0.386 AC: 16018 AN: 41450

American (AMR) AF: 0.348 AC: 5320 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1824 AN: 3468

East Asian (EAS) AF: 0.211 AC: 1094 AN: 5182

South Asian (SAS) AF: 0.342 AC: 1645 AN: 4812

European-Finnish (FIN) AF: 0.544 AC: 5745 AN: 10560

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32567 AN: 67982

Other (OTH) AF: 0.436 AC: 922 AN: 2116

Alfa AF: 0.462 Hom.: 2013

Bravo AF: 0.417

Asia WGS AF: 0.282 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	23
DANN	Benign	0.74
PhyloP100		6.7

Splicing

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

Other links and lift over

dbSNP: rs1543400; hg19: chr20-39462593;