chr6-2936688-G-T

Variant names:

• chr6-2936688-G-T
• rs318452
• ENST00000810775.1:n.275-4460G>T

Variant summary

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

The ENST00000810775.1(ENSG00000228365):​n.275-4460G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,592 control chromosomes in the GnomAD database, including 20,309 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 0.51 (20309 hom., cov: 33)
• Consequence: ENSG00000228365 ENST00000810775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 1 publications found

Genes affected

ENSG00000228365 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810775.1. 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
	ENSG00000228365	ENST00000810775.1		n.275-4460G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77401 AN: 151472 Hom.: 20264 Cov.: 33

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.511 AC: 77498 AN: 151592 Hom.: 20309 Cov.: 33 AF XY: 0.510 AC XY: 37774 AN XY: 74064

African (AFR) AF: 0.581 AC: 23994 AN: 41274

American (AMR) AF: 0.568 AC: 8685 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1808 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3781 AN: 5164

South Asian (SAS) AF: 0.517 AC: 2485 AN: 4806

European-Finnish (FIN) AF: 0.396 AC: 4162 AN: 10514

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.456 AC: 30935 AN: 67780

Other (OTH) AF: 0.544 AC: 1143 AN: 2102

Alfa AF: 0.349 Hom.: 920

Bravo AF: 0.529

Asia WGS AF: 0.636 AC: 2210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.52
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs318452; hg19: chr6-2936922;