rs35597309

Variant names:

• chr6-32621489-G-A
• rs35597309
• ENST00000843605.1:n.109+1006C>T

Variant summary

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

The ENST00000843605.1(ENSG00000309733):​n.109+1006C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0489 in 152,194 control chromosomes in the GnomAD database, including 224 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 0.049 (224 hom., cov: 32)
• Consequence: ENSG00000309733 ENST00000843605.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 12 publications found

Genes affected

ENSG00000309733 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 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
ENSG00000309733	ENST00000843605.1	n.109+1006C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7418 AN: 152076 Hom.: 222 Cov.: 32

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.0390

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0794

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0359

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0489 AC: 7436 AN: 152194 Hom.: 224 Cov.: 32 AF XY: 0.0493 AC XY: 3666 AN XY: 74406

African (AFR) AF: 0.0706 AC: 2928 AN: 41494

American (AMR) AF: 0.0390 AC: 596 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3470

East Asian (EAS) AF: 0.0790 AC: 409 AN: 5178

South Asian (SAS) AF: 0.124 AC: 596 AN: 4820

European-Finnish (FIN) AF: 0.0162 AC: 172 AN: 10600

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0359 AC: 2441 AN: 68018

Other (OTH) AF: 0.0568 AC: 120 AN: 2114

Alfa AF: 0.0418 Hom.: 22

Bravo AF: 0.0494

Asia WGS AF: 0.106 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.79
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs35597309; hg19: chr6-32589266;