6-72483449-C-A

Variant names:

• chr6-72483449-C-A
• rs1334346
• ENST00000728302.1:n.30-15516G>T

Variant summary

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

The ENST00000728302.1(ENSG00000295155):​n.30-15516G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 151,882 control chromosomes in the GnomAD database, including 35,631 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 0.67 (35631 hom., cov: 31)
• Consequence: ENSG00000295155 ENST00000728302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 6 publications found

Genes affected

ENSG00000295155 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000728302.1. 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
	ENSG00000295155	ENST00000728302.1		n.30-15516G>T		intron	N/A
	ENSG00000295155	ENST00000728303.1		n.86-15516G>T		intron	N/A
	ENSG00000295155	ENST00000728304.1		n.108-15516G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101747 AN: 151764 Hom.: 35587 Cov.: 31

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.670 AC: 101833 AN: 151882 Hom.: 35631 Cov.: 31 AF XY: 0.669 AC XY: 49625 AN XY: 74214

African (AFR) AF: 0.887 AC: 36814 AN: 41512

American (AMR) AF: 0.614 AC: 9358 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1705 AN: 3460

East Asian (EAS) AF: 0.547 AC: 2823 AN: 5158

South Asian (SAS) AF: 0.582 AC: 2799 AN: 4812

European-Finnish (FIN) AF: 0.657 AC: 6945 AN: 10568

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39360 AN: 67824

Other (OTH) AF: 0.637 AC: 1346 AN: 2112

Alfa AF: 0.567 Hom.: 3000

Bravo AF: 0.674

Asia WGS AF: 0.574 AC: 1999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.60
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1334346; hg19: chr6-73193151;