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. Variant got -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

Genes affected

ENSG00000253331 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000253331	ENST00000521805.1	n.496-35596A>T		intron_variant	Intron 4 of 4	3

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

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.963

Gnomad4 ASJ AF: 0.928

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.931

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7735506; hg19: chr5-163581878;