rs2927438

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000693032.2(ENSG00000288773):​n.1273G>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 ENST00000693032.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

Genes affected

ENSG00000288773 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.44738850G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288773	ENST00000693032.2	n.1273G>A		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.202

Alfa AF: 0.206 Hom.: 4175

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2927438; hg19: chr19-45242107;