ENST00000772883.1:n.348+7066T>C

Variant names:

• chr6-11617934-T-C
• rs479526
• ENST00000772883.1:n.348+7066T>C

Variant summary

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

The ENST00000772883.1(ENSG00000271897):​n.348+7066T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,740 control chromosomes in the GnomAD database, including 19,467 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 0.50 (19467 hom., cov: 30)
• Consequence: ENSG00000271897 ENST00000772883.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 4 publications found

Genes affected

ENSG00000271897 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772883.1. 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
	ENSG00000271897	ENST00000772883.1		n.348+7066T>C		intron	N/A
	ENSG00000271897	ENST00000772884.1		n.420-2642T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76389 AN: 151628 Hom.: 19459 Cov.: 30

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.504 AC: 76440 AN: 151740 Hom.: 19467 Cov.: 30 AF XY: 0.506 AC XY: 37547 AN XY: 74134

African (AFR) AF: 0.548 AC: 22650 AN: 41338

American (AMR) AF: 0.566 AC: 8625 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1719 AN: 3466

East Asian (EAS) AF: 0.503 AC: 2592 AN: 5154

South Asian (SAS) AF: 0.572 AC: 2748 AN: 4808

European-Finnish (FIN) AF: 0.482 AC: 5061 AN: 10490

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31316 AN: 67942

Other (OTH) AF: 0.483 AC: 1015 AN: 2102

Alfa AF: 0.462 Hom.: 23544

Bravo AF: 0.510

Asia WGS AF: 0.556 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.050
DANN	Benign	0.39
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs479526; hg19: chr6-11618167;