rs2277777

Variant names:

• chr20-16590289-T-C
• rs2277777
• ENST00000796242.1:n.1191A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000796242.1(ENSG00000303645):​n.1191A>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 0.469 in 151,838 control chromosomes in the GnomAD database, including 17,008 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 0.47 (17008 hom., cov: 32)
• Consequence: ENSG00000303645 ENST00000796242.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.766
• Publications: 9 publications found

Genes affected

ENSG00000303645 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796242.1. 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
	ENSG00000303645	ENST00000796242.1		n.1191A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71234 AN: 151720 Hom.: 17000 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.469 AC: 71280 AN: 151838 Hom.: 17008 Cov.: 32 AF XY: 0.473 AC XY: 35114 AN XY: 74200

African (AFR) AF: 0.435 AC: 17968 AN: 41276

American (AMR) AF: 0.439 AC: 6708 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1356 AN: 3464

East Asian (EAS) AF: 0.555 AC: 2860 AN: 5152

South Asian (SAS) AF: 0.480 AC: 2319 AN: 4828

European-Finnish (FIN) AF: 0.596 AC: 6294 AN: 10556

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32361 AN: 67982

Other (OTH) AF: 0.438 AC: 918 AN: 2096

Alfa AF: 0.467 Hom.: 26394

Bravo AF: 0.460

Asia WGS AF: 0.519 AC: 1804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	18
DANN	Benign	0.78
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs2277777; hg19: chr20-16570934;