rs7929679

Positions:

• chr11-34784302-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062652.1(LOC102723568):​n.1044+29695A>G variant causes a intron, non coding transcript 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: LOC102723568 XR_007062652.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659

Genes affected

LOC102723568 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723568	XR_007062652.1	n.1044+29695A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.486

Alfa AF: 0.498 Hom.: 9065

Bravo AF: 0.528

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7929679; hg19: chr11-34805849;