19-15613392-A-G

Variant names:

• chr19-15613392-A-G
• rs3764563
• ENST00000589196.2:n.457T>C

Variant summary

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

The ENST00000589196.2(ENSG00000266951):​n.457T>C 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 0.915 in 152,294 control chromosomes in the GnomAD database, including 63,776 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 0.91 (63762 hom., cov: 32)
  • Exomes 𝑓: 0.94 (14 hom.)
• Consequence: ENSG00000266951 ENST00000589196.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 10 publications found

Genes affected

ENSG00000266951 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000589196.2. 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
	ENSG00000266951	ENST00000589196.2	TSL:4	n.457T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139200 AN: 152144 Hom.: 63714 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.919

GnomAD4 exome AF: 0.938 AC: 30 AN: 32 Hom.: 14 Cov.: 0 AF XY: 0.962 AC XY: 25 AN XY: 26

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.909 AC: 20 AN: 22

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.915 AC: 139306 AN: 152262 Hom.: 63762 Cov.: 32 AF XY: 0.915 AC XY: 68116 AN XY: 74444

African (AFR) AF: 0.927 AC: 38531 AN: 41544

American (AMR) AF: 0.958 AC: 14647 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3158 AN: 3470

East Asian (EAS) AF: 0.961 AC: 4977 AN: 5178

South Asian (SAS) AF: 0.796 AC: 3843 AN: 4830

European-Finnish (FIN) AF: 0.922 AC: 9773 AN: 10602

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61351 AN: 68026

Other (OTH) AF: 0.915 AC: 1932 AN: 2112

Alfa AF: 0.906 Hom.: 218701

Bravo AF: 0.921

Asia WGS AF: 0.875 AC: 3044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.39
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs3764563; hg19: chr19-15724203;