19-50849575-T-C

Variant names:

• chr19-50849575-T-C
• rs2739448
• ENST00000598079.1:n.214-1336T>C

Variant summary

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

The ENST00000598079.1(ENSG00000267968):​n.214-1336T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,172 control chromosomes in the GnomAD database, including 3,889 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 0.21 (3889 hom., cov: 32)
• Consequence: ENSG00000267968 ENST00000598079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 4 publications found

Genes affected

ENSG00000267968 (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 = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372441	NR_131203.1	n.214-1336T>C		intron_variant	Intron 2 of 2
LOC105372441	NR_131205.1	n.231-1336T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267968	ENST00000598079.1	n.214-1336T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31299 AN: 152054 Hom.: 3885 Cov.: 32

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.202

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.206 AC: 31312 AN: 152172 Hom.: 3889 Cov.: 32 AF XY: 0.209 AC XY: 15561 AN XY: 74390

African (AFR) AF: 0.0898 AC: 3730 AN: 41530

American (AMR) AF: 0.318 AC: 4854 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3470

East Asian (EAS) AF: 0.363 AC: 1875 AN: 5164

South Asian (SAS) AF: 0.145 AC: 699 AN: 4826

European-Finnish (FIN) AF: 0.331 AC: 3499 AN: 10578

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15286 AN: 68006

Other (OTH) AF: 0.209 AC: 441 AN: 2112

Alfa AF: 0.222 Hom.: 1663

Bravo AF: 0.202

Asia WGS AF: 0.272 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2739448; hg19: chr19-51352831;