19-44912383-G-A

Variant names:

• chr19-44912383-G-A
• rs445925
• ENST00000623895.1:n.3009G>A

Variant summary

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

The ENST00000623895.1(ENSG00000280087):​n.3009G>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 0.145 in 152,156 control chromosomes in the GnomAD database, including 2,190 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 0.15 (2189 hom., cov: 32)
  • Exomes 𝑓: 0.069 (1 hom.)
• Consequence: ENSG00000280087 ENST00000623895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217
• Publications: 173 publications found

Genes affected

ENSG00000280087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623895.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000280087	ENST00000623895.1	TSL:6	n.3009G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22029 AN: 151894 Hom.: 2187 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.126

GnomAD4 exome AF: 0.0694 AC: 10 AN: 144 Hom.: 1 Cov.: 0 AF XY: 0.0510 AC XY: 5 AN XY: 98

African (AFR) AF: 0.333 AC: 2 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0667 AC: 8 AN: 120

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.145 AC: 22058 AN: 152012 Hom.: 2189 Cov.: 32 AF XY: 0.140 AC XY: 10405 AN XY: 74326

African (AFR) AF: 0.280 AC: 11597 AN: 41420

American (AMR) AF: 0.0729 AC: 1113 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3470

East Asian (EAS) AF: 0.0948 AC: 489 AN: 5160

South Asian (SAS) AF: 0.0642 AC: 309 AN: 4810

European-Finnish (FIN) AF: 0.0624 AC: 662 AN: 10604

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

European-Non Finnish (NFE) AF: 0.106 AC: 7238 AN: 67970

Other (OTH) AF: 0.127 AC: 268 AN: 2112

Alfa AF: 0.116 Hom.: 5176

Bravo AF: 0.153

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.71
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs445925; hg19: chr19-45415640;