rs10919543

Variant names:

• chr1-161538827-A-G
• rs10919543
• ENST00000537821.2:n.271+20690A>G

Variant summary

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

The ENST00000537821.2(ENSG00000273112):​n.271+20690A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 151,918 control chromosomes in the GnomAD database, including 6,507 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 0.28 (6507 hom., cov: 32)
• Consequence: ENSG00000273112 ENST00000537821.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 22 publications found

Genes affected

ENSG00000273112 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.336 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
ENSG00000273112	ENST00000537821.2	n.271+20690A>G		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42827 AN: 151800 Hom.: 6502 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.282 AC: 42849 AN: 151918 Hom.: 6507 Cov.: 32 AF XY: 0.282 AC XY: 20973 AN XY: 74244

African (AFR) AF: 0.173 AC: 7152 AN: 41428

American (AMR) AF: 0.268 AC: 4099 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1376 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1634 AN: 5186

South Asian (SAS) AF: 0.329 AC: 1583 AN: 4812

European-Finnish (FIN) AF: 0.270 AC: 2846 AN: 10538

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23043 AN: 67902

Other (OTH) AF: 0.307 AC: 647 AN: 2108

Alfa AF: 0.301 Hom.: 917

Bravo AF: 0.278

Asia WGS AF: 0.321 AC: 1116 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.85
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10919543; hg19: chr1-161508617;