rs9271568

Variant names:

• chr6-32622686-G-A
• rs9271568
• ENST00000843606.1:n.438C>T

Variant summary

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

The ENST00000843606.1(ENSG00000309733):​n.438C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,868 control chromosomes in the GnomAD database, including 6,080 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 0.27 (6080 hom., cov: 30)
• Consequence: ENSG00000309733 ENST00000843606.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 17 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843606.1. 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
	ENSG00000309733	ENST00000843606.1		n.438C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000309733	ENST00000843605.1		n.-83C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41636 AN: 151750 Hom.: 6077 Cov.: 30

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.274 AC: 41667 AN: 151868 Hom.: 6080 Cov.: 30 AF XY: 0.272 AC XY: 20169 AN XY: 74216

African (AFR) AF: 0.203 AC: 8423 AN: 41440

American (AMR) AF: 0.325 AC: 4952 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3462

East Asian (EAS) AF: 0.351 AC: 1818 AN: 5174

South Asian (SAS) AF: 0.255 AC: 1227 AN: 4810

European-Finnish (FIN) AF: 0.241 AC: 2536 AN: 10526

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20551 AN: 67896

Other (OTH) AF: 0.272 AC: 573 AN: 2106

Alfa AF: 0.264 Hom.: 623

Bravo AF: 0.285

Asia WGS AF: 0.249 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.0
DANN	Benign	0.55
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9271568; hg19: chr6-32590463;