rs11032829

chr11-34726955-T-C

Variant summary

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

The XR_007062652.1(LOC102723568):n.589-109T>C 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 0.115 in 152,166 control chromosomes in the GnomAD database, including 1,220 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 0.11 (1220 hom., cov: 32)
• Consequence: LOC102723568 XR_007062652.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

Genes affected

LOC102723568 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723568	XR_007062652.1	n.589-109T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17454 AN: 152048 Hom.: 1223 Cov.: 32

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0932

Gnomad ASJ AF: 0.0642

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.0987

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

GnomAD4 genome AF: 0.115 AC: 17461 AN: 152166 Hom.: 1220 Cov.: 32 AF XY: 0.123 AC XY: 9128 AN XY: 74382

Gnomad4 AFR AF: 0.0907

Gnomad4 AMR AF: 0.0939

Gnomad4 ASJ AF: 0.0642

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.0989

Gnomad4 OTH AF: 0.0962

Alfa AF: 0.0995 Hom.: 1141

Bravo AF: 0.104

Asia WGS AF: 0.292 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11032829; hg19: chr11-34748502;