rs686375

Positions:

• chr11-102862503-C-T

Variant summary

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

The XR_007062868.1(LOC124902741):​n.1992-2695C>T 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 0.133 in 152,164 control chromosomes in the GnomAD database, including 2,329 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 0.13 (2329 hom., cov: 32)
• Consequence: LOC124902741 XR_007062868.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401

Genes affected

LOC124902741 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902741	XR_007062868.1	n.1992-2695C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20271 AN: 152046 Hom.: 2324 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.0539

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.133 AC: 20285 AN: 152164 Hom.: 2329 Cov.: 32 AF XY: 0.131 AC XY: 9711 AN XY: 74386

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.0816

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0999

Gnomad4 FIN AF: 0.0407

Gnomad4 NFE AF: 0.0539

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0873 Hom.: 226

Bravo AF: 0.144

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.71
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs686375; hg19: chr11-102733234;