rs7735506

Variant names:

• chr5-164154872-T-A
• rs7735506
• ENST00000521805.1:n.496-35596A>T

Your query was ambiguous. Multiple possible variants found:

• chr5-164154872-T-A
• chr5-164154872-T-C
• chr5-164154872-T-G

Variant summary

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

The ENST00000521805.1(ENSG00000253331):​n.496-35596A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,122 control chromosomes in the GnomAD database, including 65,257 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 0.93 (65257 hom., cov: 31)
• Consequence: ENSG00000253331 ENST00000521805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385
• Publications: 4 publications found

Genes affected

ENSG00000253331 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521805.1. 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
	ENSG00000253331	ENST00000521805.1	TSL:3	n.496-35596A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140761 AN: 152004 Hom.: 65210 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.926 AC: 140865 AN: 152122 Hom.: 65257 Cov.: 31 AF XY: 0.928 AC XY: 69010 AN XY: 74366

African (AFR) AF: 0.913 AC: 37922 AN: 41518

American (AMR) AF: 0.963 AC: 14695 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.928 AC: 3223 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5158 AN: 5168

South Asian (SAS) AF: 0.937 AC: 4523 AN: 4826

European-Finnish (FIN) AF: 0.942 AC: 9993 AN: 10608

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62285 AN: 67946

Other (OTH) AF: 0.931 AC: 1966 AN: 2112

Alfa AF: 0.922 Hom.: 8044

Bravo AF: 0.928

Asia WGS AF: 0.958 AC: 3321 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.37
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7735506; hg19: chr5-163581878;