rs147269019

Positions:

• chr11-76754737-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The XR_950337.3(LOC105369397):​n.444+1633G>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 0.00765 in 152,188 control chromosomes in the GnomAD database, including 7 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 0.0076 (7 hom., cov: 31)
• Consequence: LOC105369397 XR_950337.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

Genes affected

LOC105369397 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369397	XR_950337.3	n.444+1633G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00765 AC: 1164 AN: 152070 Hom.: 7 Cov.: 31

Gnomad AFR AF: 0.00181

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.00820

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00641

Gnomad FIN AF: 0.00538

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0115

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

GnomAD4 genome AF: 0.00765 AC: 1164 AN: 152188 Hom.: 7 Cov.: 31 AF XY: 0.00724 AC XY: 539 AN XY: 74420

Gnomad4 AFR AF: 0.00181

Gnomad4 AMR AF: 0.00819

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00683

Gnomad4 FIN AF: 0.00538

Gnomad4 NFE AF: 0.0117

Gnomad4 OTH AF: 0.0114

Alfa AF: 0.00821 Hom.: 0

Bravo AF: 0.00791

Asia WGS AF: 0.00318 AC: 13 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	1.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs147269019; hg19: chr11-76465781;