rs704744

chr11-34715014-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.411-43A>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 0.511 in 151,962 control chromosomes in the GnomAD database, including 20,597 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 0.51 (20597 hom., cov: 31)
• Consequence: LOC102723568 XR_007062652.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807

Genes affected

LOC102723568 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723568	XR_007062652.1	n.411-43A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77613 AN: 151842 Hom.: 20572 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.511 AC: 77677 AN: 151962 Hom.: 20597 Cov.: 31 AF XY: 0.502 AC XY: 37280 AN XY: 74258

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.518

Alfa AF: 0.532 Hom.: 9980

Bravo AF: 0.503

Asia WGS AF: 0.245 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.90
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs704744; hg19: chr11-34736561;