19-44912678-G-T

Variant names:

• chr19-44912678-G-T
• rs7256200
• ENST00000623895.1:n.3304G>T

Variant summary

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

The ENST00000623895.1(ENSG00000280087):​n.3304G>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 0.133 in 152,332 control chromosomes in the GnomAD database, including 1,475 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 0.13 (1475 hom., cov: 33)
  • Exomes 𝑓: 0.12 (0 hom.)
• Consequence: ENSG00000280087 ENST00000623895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 54 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 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.3304G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20241 AN: 152102 Hom.: 1465 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.0953

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0977

GnomAD4 exome AF: 0.116 AC: 13 AN: 112 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 11 AN XY: 88

African (AFR) AF: 0.500 AC: 1 AN: 2

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

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.117 AC: 11 AN: 94

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.133 AC: 20279 AN: 152220 Hom.: 1475 Cov.: 33 AF XY: 0.136 AC XY: 10095 AN XY: 74430

African (AFR) AF: 0.189 AC: 7846 AN: 41500

American (AMR) AF: 0.0945 AC: 1446 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 324 AN: 3468

East Asian (EAS) AF: 0.0955 AC: 495 AN: 5182

South Asian (SAS) AF: 0.0652 AC: 315 AN: 4830

European-Finnish (FIN) AF: 0.174 AC: 1846 AN: 10600

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7663 AN: 68024

Other (OTH) AF: 0.0995 AC: 210 AN: 2110

Alfa AF: 0.0982 Hom.: 375

Bravo AF: 0.130

Asia WGS AF: 0.122 AC: 426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.036
DANN	Benign	0.46
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs7256200; hg19: chr19-45415935;