rs6140387

chr20-7698930-T-C

Variant summary

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

The XR_937232.1(LOC105372518):n.131+447T>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 0.2 in 151,986 control chromosomes in the GnomAD database, including 3,669 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 0.20 (3669 hom., cov: 32)
• Consequence: LOC105372518 XR_937232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

Genes affected

LOC105372518 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372518	XR_937232.1	n.131+447T>C		intron_variant, non_coding_transcript_variant
LOC105372518	XR_937230.2	n.131+447T>C		intron_variant, non_coding_transcript_variant
LOC105372518	XR_937231.1	n.131+447T>C		intron_variant, non_coding_transcript_variant
LOC105372518	XR_937233.1	n.131+447T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30356 AN: 151868 Hom.: 3665 Cov.: 32

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0223

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.200 AC: 30384 AN: 151986 Hom.: 3669 Cov.: 32 AF XY: 0.203 AC XY: 15091 AN XY: 74272

Gnomad4 AFR AF: 0.0815

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.0227

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.194

Alfa AF: 0.237 Hom.: 576

Bravo AF: 0.181

Asia WGS AF: 0.122 AC: 429 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.10
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6140387; hg19: chr20-7679577;