chr20-7674292-C-A

Variant names:

• chr20-7674292-C-A
• rs6140378
• ENST00000839999.1:n.397-5293G>T

Variant summary

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

The ENST00000839999.1(ENSG00000309276):​n.397-5293G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,096 control chromosomes in the GnomAD database, including 2,994 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 0.17 (2994 hom., cov: 33)
• Consequence: ENSG00000309276 ENST00000839999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607
• Publications: 4 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 = 0.594 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309276	ENST00000839999.1		n.397-5293G>T		intron	N/A
	ENSG00000309276	ENST00000840000.1		n.76-5293G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26495 AN: 151976 Hom.: 2995 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.0928

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.174 AC: 26512 AN: 152096 Hom.: 2994 Cov.: 33 AF XY: 0.176 AC XY: 13096 AN XY: 74334

African (AFR) AF: 0.190 AC: 7900 AN: 41482

American (AMR) AF: 0.145 AC: 2214 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3470

East Asian (EAS) AF: 0.612 AC: 3158 AN: 5162

South Asian (SAS) AF: 0.355 AC: 1710 AN: 4816

European-Finnish (FIN) AF: 0.0928 AC: 983 AN: 10590

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9401 AN: 67992

Other (OTH) AF: 0.182 AC: 385 AN: 2110

Alfa AF: 0.158 Hom.: 5359

Bravo AF: 0.181

Asia WGS AF: 0.446 AC: 1550 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	0.41
DANN	Benign	0.25
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs6140378; hg19: chr20-7654939;