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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372646	XR_936817.4	n.793A>G		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294979	ENST00000727174.1	n.549A>G		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000294979	ENST00000727175.1	n.790A>G		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000294963	ENST00000727053.1	n.*243T>C		downstream_gene_variant

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 v4.3

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;