rs7929679

Variant names:

• chr11-34784302-A-G
• rs7929679
• ENST00000843048.1:n.656+29695A>G

Variant summary

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

The ENST00000843048.1(ENSG00000309692):​n.656+29695A>G 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 151,406 control chromosomes in the GnomAD database, including 21,913 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 (21913 hom., cov: 31)
• Consequence: ENSG00000309692 ENST00000843048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659
• Publications: 17 publications found

Genes affected

ENSG00000309692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843048.1. 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
	ENSG00000309692	ENST00000843048.1		n.656+29695A>G		intron	N/A
	ENSG00000309692	ENST00000843049.1		n.848+29695A>G		intron	N/A
	ENSG00000309692	ENST00000843050.1		n.440+29695A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80116 AN: 151288 Hom.: 21890 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.530 AC: 80175 AN: 151406 Hom.: 21913 Cov.: 31 AF XY: 0.525 AC XY: 38865 AN XY: 73986

African (AFR) AF: 0.669 AC: 27553 AN: 41174

American (AMR) AF: 0.402 AC: 6121 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1434 AN: 3472

East Asian (EAS) AF: 0.427 AC: 2193 AN: 5138

South Asian (SAS) AF: 0.396 AC: 1906 AN: 4810

European-Finnish (FIN) AF: 0.538 AC: 5652 AN: 10500

Middle Eastern (MID) AF: 0.434 AC: 125 AN: 288

European-Non Finnish (NFE) AF: 0.497 AC: 33717 AN: 67776

Other (OTH) AF: 0.486 AC: 1020 AN: 2100

Alfa AF: 0.505 Hom.: 36782

Bravo AF: 0.528

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.49
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs7929679; hg19: chr11-34805849;