rs11760067

chr6-134773134-C-T

Variant summary

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

The XR_001744364.2(LOC101928277):n.342+32604G>A 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 0.074 in 151,786 control chromosomes in the GnomAD database, including 569 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 0.074 (569 hom., cov: 27)
• Consequence: LOC101928277 XR_001744364.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

Genes affected

LOC101928277 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928277	XR_001744364.2	n.342+32604G>A		intron_variant, non_coding_transcript_variant
LOC101928277	XR_001744363.2	n.395+32604G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0741 AC: 11235 AN: 151668 Hom.: 568 Cov.: 27

Gnomad AFR AF: 0.0194

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0468

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0833

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

GnomAD4 genome AF: 0.0740 AC: 11231 AN: 151786 Hom.: 569 Cov.: 27 AF XY: 0.0720 AC XY: 5340 AN XY: 74190

Gnomad4 AFR AF: 0.0194

Gnomad4 AMR AF: 0.0743

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0471

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0719

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0819

Alfa AF: 0.0796 Hom.: 103

Bravo AF: 0.0712

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.9
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11760067; hg19: chr6-135094272;