rs2927438

Variant names:

• chr19-44738850-G-A
• rs2927438
• ENST00000693032.3:n.1274G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-44738850-G-A
• chr19-44738850-G-T

Variant summary

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

The ENST00000693032.3(ENSG00000288773):​n.1274G>A 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 0.196 in 152,106 control chromosomes in the GnomAD database, including 3,061 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 0.20 (3061 hom., cov: 32)
• Consequence: ENSG00000288773 ENST00000693032.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 32 publications found

Genes affected

ENSG00000288773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 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
ENSG00000288773	ENST00000693032.3	n.1274G>A		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000288773	ENST00000790574.1	n.717G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000288773	ENST00000790564.1	n.156+1008G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29739 AN: 151990 Hom.: 3060 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.196 AC: 29755 AN: 152106 Hom.: 3061 Cov.: 32 AF XY: 0.198 AC XY: 14716 AN XY: 74336

African (AFR) AF: 0.138 AC: 5740 AN: 41518

American (AMR) AF: 0.190 AC: 2900 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 793 AN: 3460

East Asian (EAS) AF: 0.233 AC: 1202 AN: 5150

South Asian (SAS) AF: 0.198 AC: 957 AN: 4830

European-Finnish (FIN) AF: 0.283 AC: 3002 AN: 10590

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.213 AC: 14456 AN: 67956

Other (OTH) AF: 0.202 AC: 426 AN: 2114

Alfa AF: 0.207 Hom.: 4948

Bravo AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.4
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs2927438; hg19: chr19-45242107;