19-44909976-G-T

Variant names:

• chr19-44909976-G-T
• rs1065853
• ENST00000623895.1:n.602G>T

Variant summary

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

The ENST00000623895.1(ENSG00000280087):​n.602G>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 0.0809 in 151,942 control chromosomes in the GnomAD database, including 631 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 0.081 (629 hom., cov: 31)
  • Exomes 𝑓: 0.042 (2 hom.)
• Consequence: ENSG00000280087 ENST00000623895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 47 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 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.602G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0810 AC: 12261 AN: 151288 Hom.: 629 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0698

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.0367

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.0812

GnomAD4 exome AF: 0.0424 AC: 23 AN: 542 Hom.: 2 Cov.: 0 AF XY: 0.0395 AC XY: 14 AN XY: 354

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 42

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 22

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0505 AC: 22 AN: 436

Other (OTH) AF: 0.0417 AC: 1 AN: 24

GnomAD4 genome AF: 0.0810 AC: 12269 AN: 151400 Hom.: 629 Cov.: 31 AF XY: 0.0773 AC XY: 5718 AN XY: 73982

African (AFR) AF: 0.115 AC: 4717 AN: 41146

American (AMR) AF: 0.0438 AC: 665 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.0698 AC: 242 AN: 3468

East Asian (EAS) AF: 0.0811 AC: 418 AN: 5154

South Asian (SAS) AF: 0.0371 AC: 177 AN: 4768

European-Finnish (FIN) AF: 0.0421 AC: 444 AN: 10546

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0797 AC: 5409 AN: 67832

Other (OTH) AF: 0.0823 AC: 172 AN: 2090

Alfa AF: 0.0372 Hom.: 34

Bravo AF: 0.0814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.40
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1065853; hg19: chr19-45413233;