11-38263951-T-C

Position:

• chr11-38263951-T-C

Variant summary

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

The XR_931202.2(LOC105376634):​n.554+61224A>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 0.786 in 151,970 control chromosomes in the GnomAD database, including 51,407 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 0.79 (51407 hom., cov: 32)
• Consequence: LOC105376634 XR_931202.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

Genes affected

LOC105376634 (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 = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376634	XR_931202.2	n.554+61224A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119373 AN: 151852 Hom.: 51403 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.786 AC: 119402 AN: 151970 Hom.: 51407 Cov.: 32 AF XY: 0.787 AC XY: 58432 AN XY: 74260

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.892

Gnomad4 ASJ AF: 0.960

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.958

Gnomad4 OTH AF: 0.835

Alfa AF: 0.933 Hom.: 127502

Bravo AF: 0.767

Asia WGS AF: 0.782 AC: 2721 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10836945; hg19: chr11-38285501;