chr11-76559639-A-G

Variant names:

• chr11-76559639-A-G
• rs7130588
• ENST00000830356.1:n.399-3994T>C

Variant summary

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

The ENST00000830356.1(ENSG00000308001):​n.399-3994T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,036 control chromosomes in the GnomAD database, including 6,600 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 0.29 (6600 hom., cov: 31)
• Consequence: ENSG00000308001 ENST00000830356.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543
• Publications: 65 publications found

Genes affected

ENSG00000308001 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830356.1. 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
	ENSG00000308001	ENST00000830356.1		n.399-3994T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43341 AN: 151918 Hom.: 6601 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.285 AC: 43355 AN: 152036 Hom.: 6600 Cov.: 31 AF XY: 0.279 AC XY: 20768 AN XY: 74324

African (AFR) AF: 0.204 AC: 8456 AN: 41462

American (AMR) AF: 0.244 AC: 3730 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1442 AN: 3468

East Asian (EAS) AF: 0.0927 AC: 479 AN: 5166

South Asian (SAS) AF: 0.230 AC: 1107 AN: 4820

European-Finnish (FIN) AF: 0.277 AC: 2925 AN: 10562

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23950 AN: 67986

Other (OTH) AF: 0.310 AC: 652 AN: 2104

Alfa AF: 0.330 Hom.: 40121

Bravo AF: 0.283

Asia WGS AF: 0.165 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.78
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs7130588; hg19: chr11-76270683;