rs6140410

Variant names:

• chr20-7756893-T-C
• rs6140410
• ENST00000839999.1:n.283-17967A>G

Variant summary

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

The ENST00000839999.1(ENSG00000309276):​n.283-17967A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,212 control chromosomes in the GnomAD database, including 1,281 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 0.13 (1281 hom., cov: 32)
• Consequence: ENSG00000309276 ENST00000839999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839999.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309276	ENST00000839999.1		n.283-17967A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19089 AN: 152096 Hom.: 1280 Cov.: 32

Gnomad AFR AF: 0.0711

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.125 AC: 19089 AN: 152212 Hom.: 1281 Cov.: 32 AF XY: 0.126 AC XY: 9350 AN XY: 74422

African (AFR) AF: 0.0710 AC: 2950 AN: 41538

American (AMR) AF: 0.127 AC: 1944 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3466

East Asian (EAS) AF: 0.161 AC: 829 AN: 5162

South Asian (SAS) AF: 0.158 AC: 761 AN: 4830

European-Finnish (FIN) AF: 0.150 AC: 1590 AN: 10600

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9832 AN: 68004

Other (OTH) AF: 0.133 AC: 282 AN: 2114

Alfa AF: 0.146 Hom.: 1427

Bravo AF: 0.123

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.96
DANN	Benign	0.46
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6140410; hg19: chr20-7737540;