11-104346753-T-C

Position:

• chr11-104346753-T-C

Variant summary

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

The XR_428991.3(LOC102723879):​n.290+7609T>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 0.441 in 152,042 control chromosomes in the GnomAD database, including 14,971 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 0.44 (14971 hom., cov: 33)
• Consequence: LOC102723879 XR_428991.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

LOC102723879 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723879	XR_428991.3	n.290+7609T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67037 AN: 151924 Hom.: 14940 Cov.: 33

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.441 AC: 67119 AN: 152042 Hom.: 14971 Cov.: 33 AF XY: 0.440 AC XY: 32690 AN XY: 74292

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.446

Alfa AF: 0.436 Hom.: 15977

Bravo AF: 0.437

Asia WGS AF: 0.482 AC: 1676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10895656; hg19: chr11-104217481;