2-20971074-G-A

Variant names:

• chr2-20971074-G-A
• rs6728178
• ENST00000764419.1:n.-135G>A

Variant summary

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

The ENST00000764419.1(ENSG00000299535):​n.-135G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,184 control chromosomes in the GnomAD database, including 5,842 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 0.26 (5842 hom., cov: 33)
• Consequence: ENSG00000299535 ENST00000764419.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 21 publications found

Genes affected

ENSG00000299535 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299535	ENST00000764419.1	n.-135G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38897 AN: 152066 Hom.: 5845 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.256 AC: 38903 AN: 152184 Hom.: 5842 Cov.: 33 AF XY: 0.262 AC XY: 19502 AN XY: 74392

African (AFR) AF: 0.200 AC: 8310 AN: 41516

American (AMR) AF: 0.234 AC: 3583 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3472

East Asian (EAS) AF: 0.718 AC: 3718 AN: 5178

South Asian (SAS) AF: 0.524 AC: 2530 AN: 4828

European-Finnish (FIN) AF: 0.274 AC: 2894 AN: 10574

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16068 AN: 68002

Other (OTH) AF: 0.253 AC: 535 AN: 2112

Alfa AF: 0.242 Hom.: 8108

Bravo AF: 0.250

Asia WGS AF: 0.586 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.68
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs6728178; hg19: chr2-21193946;