rs1581492

Variant names:

• chr7-99589203-G-A
• rs1581492
• ENST00000455905.1:n.137-11005G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-99589203-G-A
• chr7-99589203-G-T

Variant summary

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

The ENST00000455905.1(ENSG00000272647):​n.137-11005G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 150,500 control chromosomes in the GnomAD database, including 1,553 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 0.13 (1553 hom., cov: 31)
• Consequence: ENSG00000272647 ENST00000455905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

ENSG00000272647 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 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
ENSG00000272647	ENST00000455905.1	n.137-11005G>A		intron_variant	Intron 2 of 5	3		ENSP00000401282.1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 18940 AN: 150376 Hom.: 1544 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0987

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.00394

Gnomad SAS AF: 0.0682

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0646

Gnomad NFE AF: 0.0832

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.126 AC: 18978 AN: 150500 Hom.: 1553 Cov.: 31 AF XY: 0.128 AC XY: 9435 AN XY: 73482

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.0985

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.00395

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.0832

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0741 Hom.: 166

Bravo AF: 0.125

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1581492; hg19: chr7-99186826;