19-54260121-A-G

Variant names:

• chr19-54260121-A-G
• rs595872
• ENST00000767884.1:n.181+2024A>G

Variant summary

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

The ENST00000767884.1(ENSG00000299998):​n.181+2024A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,170 control chromosomes in the GnomAD database, including 47,179 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 0.78 (47176 hom., cov: 32)
  • Exomes 𝑓: 1.0 (3 hom.)
• Consequence: ENSG00000299998 ENST00000767884.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 12 publications found

Genes affected

ENSG00000299998 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 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
ENSG00000299998	ENST00000767884.1	n.181+2024A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119022 AN: 152046 Hom.: 47152 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.813

GnomAD4 exome AF: 1.00 AC: 6 AN: 6 Hom.: 3 Cov.: 0 AF XY: 1.00 AC XY: 4 AN XY: 4

African (AFR) AC: 0 AN: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.783 AC: 119103 AN: 152164 Hom.: 47176 Cov.: 32 AF XY: 0.779 AC XY: 57923 AN XY: 74394

African (AFR) AF: 0.838 AC: 34780 AN: 41526

American (AMR) AF: 0.775 AC: 11841 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2839 AN: 3468

East Asian (EAS) AF: 0.385 AC: 1989 AN: 5172

South Asian (SAS) AF: 0.749 AC: 3611 AN: 4820

European-Finnish (FIN) AF: 0.738 AC: 7813 AN: 10588

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53460 AN: 67994

Other (OTH) AF: 0.807 AC: 1705 AN: 2112

Alfa AF: 0.787 Hom.: 119510

Bravo AF: 0.781

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs595872; hg19: chr19-54763969;