rs6140387

Variant names:

• chr20-7698930-T-C
• rs6140387
• ENST00000839999.1:n.396+23957A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000839999.1(ENSG00000309276):​n.396+23957A>G variant causes a intron 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: ENSG00000309276 ENST00000839999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 1 publications found

Genes affected

ENSG00000309276 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105372518	XR_937230.2	n.131+447T>C		intron_variant	Intron 1 of 3
LOC105372518	XR_937231.1	n.131+447T>C		intron_variant	Intron 1 of 2
LOC105372518	XR_937232.1	n.131+447T>C		intron_variant	Intron 1 of 2
LOC105372518	XR_937233.1	n.131+447T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309276	ENST00000839999.1	n.396+23957A>G		intron_variant	Intron 3 of 4
ENSG00000309276	ENST00000840000.1	n.75+4691A>G		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.0815 AC: 3383 AN: 41528

American (AMR) AF: 0.214 AC: 3263 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3466

East Asian (EAS) AF: 0.0227 AC: 117 AN: 5154

South Asian (SAS) AF: 0.208 AC: 999 AN: 4812

European-Finnish (FIN) AF: 0.313 AC: 3301 AN: 10544

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17761 AN: 67926

Other (OTH) AF: 0.194 AC: 408 AN: 2104

Alfa AF: 0.231 Hom.: 580

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6140387; hg19: chr20-7679577;