rs626729

chr11-102862639-T-C

Variant summary

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

The XR_007062868.1(LOC124902741):n.1992-2559T>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 0.109 in 152,392 control chromosomes in the GnomAD database, including 1,357 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 (1357 hom., cov: 32)
  • Exomes 𝑓: 0.018 (0 hom.)
• Consequence: LOC124902741 XR_007062868.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

LOC124902741 (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 = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902741	XR_007062868.1	n.1992-2559T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16539 AN: 152166 Hom.: 1353 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.0406

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0529

Gnomad OTH AF: 0.107

GnomAD4 exome AF: 0.0182 AC: 2 AN: 110 Hom.: 0 AF XY: 0.0270 AC XY: 2 AN XY: 74

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0114

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.109 AC: 16543 AN: 152282 Hom.: 1357 Cov.: 32 AF XY: 0.107 AC XY: 7933 AN XY: 74472

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0740

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0983

Gnomad4 FIN AF: 0.0406

Gnomad4 NFE AF: 0.0529

Gnomad4 OTH AF: 0.110

Alfa AF: 0.103 Hom.: 233

Bravo AF: 0.116

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.069
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs626729; hg19: chr11-102733370;