6-155376684-A-T

Variant names:

• chr6-155376684-A-T
• rs9322519
• ENST00000809830.1:n.58-1340A>T

Variant summary

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

The ENST00000809830.1(ENSG00000305252):​n.58-1340A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,998 control chromosomes in the GnomAD database, including 5,841 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 0.26 (5841 hom., cov: 32)
• Consequence: ENSG00000305252 ENST00000809830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 2 publications found

Genes affected

ENSG00000305252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809830.1. 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
	ENSG00000305252	ENST00000809830.1		n.58-1340A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39599 AN: 151878 Hom.: 5818 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.261 AC: 39670 AN: 151998 Hom.: 5841 Cov.: 32 AF XY: 0.269 AC XY: 20000 AN XY: 74278

African (AFR) AF: 0.368 AC: 15252 AN: 41436

American (AMR) AF: 0.343 AC: 5236 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1776 AN: 5166

South Asian (SAS) AF: 0.289 AC: 1395 AN: 4824

European-Finnish (FIN) AF: 0.311 AC: 3281 AN: 10544

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11429 AN: 67978

Other (OTH) AF: 0.273 AC: 573 AN: 2102

Alfa AF: 0.129 Hom.: 236

Bravo AF: 0.270

Asia WGS AF: 0.378 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.4
DANN	Benign	0.76
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs9322519; hg19: chr6-155697818;