1-190491143-G-A

Variant names:

• chr1-190491143-G-A
• rs11581737
• ENST00000417409.1:n.47-2695G>A

Variant summary

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

The ENST00000417409.1(ENSG00000241505):​n.47-2695G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 150,574 control chromosomes in the GnomAD database, including 2,044 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 0.16 (2044 hom., cov: 31)
• Consequence: ENSG00000241505 ENST00000417409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789
• Publications: 0 publications found

Genes affected

ENSG00000241505 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417409.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000241505	ENST00000417409.1	TSL:3	n.47-2695G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23819 AN: 150484 Hom.: 2037 Cov.: 31

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.158 AC: 23829 AN: 150574 Hom.: 2044 Cov.: 31 AF XY: 0.161 AC XY: 11834 AN XY: 73448

African (AFR) AF: 0.103 AC: 4264 AN: 41206

American (AMR) AF: 0.150 AC: 2265 AN: 15066

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1106 AN: 5120

South Asian (SAS) AF: 0.219 AC: 1046 AN: 4786

European-Finnish (FIN) AF: 0.219 AC: 2199 AN: 10054

Middle Eastern (MID) AF: 0.170 AC: 49 AN: 288

European-Non Finnish (NFE) AF: 0.175 AC: 11832 AN: 67588

Other (OTH) AF: 0.125 AC: 262 AN: 2088

Alfa AF: 0.165 Hom.: 455

Bravo AF: 0.150

Asia WGS AF: 0.188 AC: 650 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.24
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs11581737; hg19: chr1-190460273;