rs7766029

Variant names:

• chr6-88137716-T-C
• rs7766029
• ENST00000756364.1:n.128+12119T>C

Variant summary

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

The ENST00000756364.1(ENSG00000298549):​n.128+12119T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,078 control chromosomes in the GnomAD database, including 19,616 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 (19616 hom., cov: 33)
• Consequence: ENSG00000298549 ENST00000756364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 43 publications found

Genes affected

ENSG00000298549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756364.1. 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
	ENSG00000298549	ENST00000756364.1		n.128+12119T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75581 AN: 151960 Hom.: 19624 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.0876

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.497 AC: 75595 AN: 152078 Hom.: 19616 Cov.: 33 AF XY: 0.492 AC XY: 36599 AN XY: 74348

African (AFR) AF: 0.511 AC: 21204 AN: 41478

American (AMR) AF: 0.371 AC: 5666 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1471 AN: 3470

East Asian (EAS) AF: 0.0874 AC: 453 AN: 5182

South Asian (SAS) AF: 0.409 AC: 1974 AN: 4824

European-Finnish (FIN) AF: 0.604 AC: 6379 AN: 10556

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36989 AN: 67976

Other (OTH) AF: 0.462 AC: 972 AN: 2104

Alfa AF: 0.519 Hom.: 13045

Bravo AF: 0.479

Asia WGS AF: 0.285 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.3
DANN	Benign	0.81
PhyloP100		-0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7766029;

hg19: chr6-88847435;