chr19-44912921-G-T

Variant names:

• chr19-44912921-G-T
• rs483082
• ENST00000623895.1:n.3547G>T

Variant summary

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

The ENST00000623895.1(ENSG00000280087):​n.3547G>T 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 0.273 in 152,284 control chromosomes in the GnomAD database, including 6,692 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 0.27 (6691 hom., cov: 32)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: ENSG00000280087 ENST00000623895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 57 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 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
ENSG00000280087	ENST00000623895.1	n.3547G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41476 AN: 151906 Hom.: 6672 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.225

GnomAD4 exome AF: 0.119 AC: 31 AN: 260 Hom.: 1 Cov.: 0 AF XY: 0.120 AC XY: 24 AN XY: 200

African (AFR) AF: 0.375 AC: 3 AN: 8

American (AMR) AF: 0.250 AC: 1 AN: 4

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

East Asian (EAS) AF: 0.125 AC: 1 AN: 8

South Asian (SAS) AF: 0.0833 AC: 1 AN: 12

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

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

European-Non Finnish (NFE) AF: 0.109 AC: 22 AN: 202

Other (OTH) AF: 0.00 AC: 0 AN: 14

GnomAD4 genome AF: 0.273 AC: 41547 AN: 152024 Hom.: 6691 Cov.: 32 AF XY: 0.270 AC XY: 20079 AN XY: 74300

African (AFR) AF: 0.449 AC: 18596 AN: 41442

American (AMR) AF: 0.167 AC: 2547 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3472

East Asian (EAS) AF: 0.191 AC: 985 AN: 5154

South Asian (SAS) AF: 0.141 AC: 679 AN: 4828

European-Finnish (FIN) AF: 0.237 AC: 2504 AN: 10586

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.219 AC: 14911 AN: 67944

Other (OTH) AF: 0.230 AC: 486 AN: 2114

Alfa AF: 0.282 Hom.: 994

Bravo AF: 0.276

Asia WGS AF: 0.255 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.5
DANN	Benign	0.84
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs483082; hg19: chr19-45416178;