rs7535666

Variant names:

• chr1-181855875-T-G
• rs7535666
• ENST00000717053.1:n.288-20239A>C

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.288-20239A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,026 control chromosomes in the GnomAD database, including 4,414 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 0.23 (4414 hom., cov: 32)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.650
• Publications: 3 publications found

Genes affected

ENSG00000287452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717053.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287452	ENST00000717053.1		n.288-20239A>C		intron	N/A
	ENSG00000287452	ENST00000717054.1		n.293-20239A>C		intron	N/A
	ENSG00000287452	ENST00000717055.1		n.81-20239A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35186 AN: 151908 Hom.: 4414 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.232 AC: 35197 AN: 152026 Hom.: 4414 Cov.: 32 AF XY: 0.231 AC XY: 17188 AN XY: 74304

African (AFR) AF: 0.141 AC: 5837 AN: 41510

American (AMR) AF: 0.271 AC: 4140 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 949 AN: 3468

East Asian (EAS) AF: 0.158 AC: 818 AN: 5162

South Asian (SAS) AF: 0.151 AC: 726 AN: 4808

European-Finnish (FIN) AF: 0.311 AC: 3289 AN: 10566

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18667 AN: 67938

Other (OTH) AF: 0.236 AC: 497 AN: 2110

Alfa AF: 0.245 Hom.: 954

Bravo AF: 0.227

Asia WGS AF: 0.171 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.9
DANN	Benign	0.60
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs7535666; hg19: chr1-181825010;