rs11581737

Positions:

• chr1-190491143-G-A
• chr1-190491143-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000417409.1(ENSG00000241505):​n.47-2695G>A variant causes a intron, non coding transcript 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: ENST00000417409.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000417409.1	n.47-2695G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.125

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11581737; hg19: chr1-190460273;