6-95659338-G-A

Variant names:

• chr6-95659338-G-A
• rs4629688
• ENST00000809528.1:n.181-464C>T

Variant summary

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

The ENST00000809528.1(ENSG00000305202):​n.181-464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,024 control chromosomes in the GnomAD database, including 55,638 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 0.85 (55638 hom., cov: 32)
• Consequence: ENSG00000305202 ENST00000809528.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810
• Publications: 1 publications found

Genes affected

ENSG00000305202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809528.1. 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
	ENSG00000305202	ENST00000809528.1		n.181-464C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129676 AN: 151906 Hom.: 55597 Cov.: 32

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.854 AC: 129772 AN: 152024 Hom.: 55638 Cov.: 32 AF XY: 0.852 AC XY: 63320 AN XY: 74304

African (AFR) AF: 0.915 AC: 37999 AN: 41518

American (AMR) AF: 0.852 AC: 13005 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3224 AN: 3466

East Asian (EAS) AF: 0.878 AC: 4495 AN: 5120

South Asian (SAS) AF: 0.903 AC: 4357 AN: 4826

European-Finnish (FIN) AF: 0.776 AC: 8234 AN: 10604

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55638 AN: 67908

Other (OTH) AF: 0.879 AC: 1855 AN: 2110

Alfa AF: 0.832 Hom.: 9228

Bravo AF: 0.864

Asia WGS AF: 0.885 AC: 3080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.55
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs4629688; hg19: chr6-96107214;