11-34434641-T-C

Position:

• chr11-34434641-T-C

Variant summary

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

The XR_931180.3(LOC105376622):​n.265+1524T>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 0.873 in 152,216 control chromosomes in the GnomAD database, including 58,430 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 0.87 (58430 hom., cov: 32)
• Consequence: LOC105376622 XR_931180.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

LOC105376622 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.11).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376622	XR_931180.3	n.265+1524T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132723 AN: 152098 Hom.: 58378 Cov.: 32

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.873 AC: 132828 AN: 152216 Hom.: 58430 Cov.: 32 AF XY: 0.872 AC XY: 64867 AN XY: 74408

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.935

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.874

Alfa AF: 0.846 Hom.: 110417

Bravo AF: 0.873

Asia WGS AF: 0.958 AC: 3332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs554518; hg19: chr11-34456188;