ENST00000808970.1:n.226-29876C>A

Variant names:

• chr6-1448886-G-T
• rs2745636
• ENST00000808970.1:n.226-29876C>A

Variant summary

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

The ENST00000808970.1(ENSG00000272279):​n.226-29876C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,034 control chromosomes in the GnomAD database, including 21,786 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 0.53 (21786 hom., cov: 33)
• Consequence: ENSG00000272279 ENST00000808970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 7 publications found

Genes affected

ENSG00000272279 (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 (EAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808970.1. 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
	ENSG00000272279	ENST00000808970.1		n.226-29876C>A		intron	N/A
	ENSG00000272279	ENST00000808971.1		n.181-24123C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80567 AN: 151916 Hom.: 21776 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.530 AC: 80617 AN: 152034 Hom.: 21786 Cov.: 33 AF XY: 0.533 AC XY: 39573 AN XY: 74290

African (AFR) AF: 0.461 AC: 19108 AN: 41486

American (AMR) AF: 0.641 AC: 9787 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3468

East Asian (EAS) AF: 0.663 AC: 3439 AN: 5188

South Asian (SAS) AF: 0.608 AC: 2931 AN: 4822

European-Finnish (FIN) AF: 0.492 AC: 5177 AN: 10524

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37251 AN: 67966

Other (OTH) AF: 0.494 AC: 1039 AN: 2102

Alfa AF: 0.540 Hom.: 78849

Bravo AF: 0.537

Asia WGS AF: 0.615 AC: 2138 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	1.4
DANN	Benign	0.61
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2745636; hg19: chr6-1449121;