11-39887112-T-C

Position:

• chr11-39887112-T-C

Variant summary

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

The XR_001748194.1(LOC105376637):​n.58+76049A>G 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 0.102 in 151,720 control chromosomes in the GnomAD database, including 999 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 0.10 (999 hom., cov: 31)
• Consequence: LOC105376637 XR_001748194.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462

Genes affected

LOC105376637 (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 = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376637	XR_001748194.1	n.58+76049A>G		intron_variant, non_coding_transcript_variant
LOC105376637	XR_001748195.2	n.58+76049A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15513 AN: 151614 Hom.: 996 Cov.: 31

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.0828

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.102 AC: 15521 AN: 151720 Hom.: 999 Cov.: 31 AF XY: 0.0994 AC XY: 7373 AN XY: 74140

Gnomad4 AFR AF: 0.0455

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0554

Gnomad4 FIN AF: 0.0828

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.142

Alfa AF: 0.139 Hom.: 1630

Bravo AF: 0.103

Asia WGS AF: 0.0480 AC: 168 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.26
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11035577; hg19: chr11-39908662;