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. The variant received -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
• Publications: 9 publications found

Genes affected

ENSG00000272647 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455905.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272647	ENST00000455905.1	TSL:3	n.137-11005G>A		intron	N/A	ENSP00000401282.1	F8WEM9

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

African (AFR) AF: 0.226 AC: 9256 AN: 41010

American (AMR) AF: 0.0985 AC: 1483 AN: 15052

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 259 AN: 3446

East Asian (EAS) AF: 0.00395 AC: 20 AN: 5062

South Asian (SAS) AF: 0.0686 AC: 328 AN: 4778

European-Finnish (FIN) AF: 0.162 AC: 1697 AN: 10482

Middle Eastern (MID) AF: 0.0761 AC: 21 AN: 276

European-Non Finnish (NFE) AF: 0.0832 AC: 5604 AN: 67390

Other (OTH) AF: 0.124 AC: 259 AN: 2094

Alfa AF: 0.0810 Hom.: 314

Bravo AF: 0.125

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.57
PhyloP100		0.064

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

Other links and lift over

dbSNP: rs1581492; hg19: chr7-99186826;