11-76567214-T-C

Variant names:

• chr11-76567214-T-C
• rs7936562
• ENST00000830356.1:n.398+6127A>G

Variant summary

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

The ENST00000830356.1(ENSG00000308001):​n.398+6127A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,120 control chromosomes in the GnomAD database, including 26,089 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 0.58 (26089 hom., cov: 32)
• Consequence: ENSG00000308001 ENST00000830356.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308001	ENST00000830356.1		n.398+6127A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88678 AN: 152002 Hom.: 26076 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.583 AC: 88732 AN: 152120 Hom.: 26089 Cov.: 32 AF XY: 0.579 AC XY: 43098 AN XY: 74376

African (AFR) AF: 0.614 AC: 25459 AN: 41492

American (AMR) AF: 0.511 AC: 7803 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2424 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2749 AN: 5176

South Asian (SAS) AF: 0.500 AC: 2414 AN: 4826

European-Finnish (FIN) AF: 0.575 AC: 6085 AN: 10574

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39763 AN: 67988

Other (OTH) AF: 0.585 AC: 1237 AN: 2114

Alfa AF: 0.583 Hom.: 80878

Bravo AF: 0.583

Asia WGS AF: 0.493 AC: 1715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.35
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs7936562; hg19: chr11-76278258;