rs7268640

Variant names:

• chr20-48533730-T-C
• rs7268640
• ENST00000727174.1:n.549A>G

Variant summary

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

The ENST00000727174.1(ENSG00000294979):​n.549A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,232 control chromosomes in the GnomAD database, including 6,400 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 (6400 hom., cov: 32)
• Consequence: ENSG00000294979 ENST00000727174.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 2 publications found

Genes affected

ENSG00000294979 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727174.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294979	ENST00000727174.1		n.549A>G		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000294979	ENST00000727175.1		n.790A>G		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000294963	ENST00000727053.1		n.*243T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26316 AN: 152114 Hom.: 6364 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0930

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.0690

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0114

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.173 AC: 26408 AN: 152232 Hom.: 6400 Cov.: 32 AF XY: 0.170 AC XY: 12634 AN XY: 74454

African (AFR) AF: 0.543 AC: 22513 AN: 41488

American (AMR) AF: 0.0930 AC: 1423 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3472

East Asian (EAS) AF: 0.178 AC: 922 AN: 5182

South Asian (SAS) AF: 0.0690 AC: 333 AN: 4824

European-Finnish (FIN) AF: 0.0111 AC: 118 AN: 10626

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0114 AC: 776 AN: 68016

Other (OTH) AF: 0.113 AC: 238 AN: 2112

Alfa AF: 0.0787 Hom.: 6352

Bravo AF: 0.199

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.35
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7268640; hg19: chr20-47150268;