rs6040399

chr20-11176363-A-T

Variant summary

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

The XR_937260.2(LOC105372528):n.168+213T>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 0.689 in 151,792 control chromosomes in the GnomAD database, including 36,377 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 0.69 (36377 hom., cov: 32)
• Consequence: LOC105372528 XR_937260.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

Genes affected

LOC105372528 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372528	XR_937260.2	n.168+213T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104499 AN: 151674 Hom.: 36341 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.689 AC: 104585 AN: 151792 Hom.: 36377 Cov.: 32 AF XY: 0.685 AC XY: 50785 AN XY: 74148

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.706

Alfa AF: 0.709 Hom.: 21240

Bravo AF: 0.674

Asia WGS AF: 0.603 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.2
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: rs6040399; hg19: chr20-11157011;