chr19-28645675-T-C

Variant names:

• chr19-28645675-T-C
• rs10401833
• ENST00000592347.5:n.642+76895A>G

Variant summary

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

The ENST00000592347.5(ENSG00000290606):​n.642+76895A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,118 control chromosomes in the GnomAD database, including 11,003 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 0.34 (11003 hom., cov: 33)
• Consequence: ENSG00000290606 ENST00000592347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807
• Publications: 0 publications found

Genes affected

ENSG00000290606 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592347.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100420587	NR_110759.1		n.656+76895A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290606	ENST00000592347.5	TSL:1	n.642+76895A>G		intron	N/A
	ENSG00000290606	ENST00000585394.1	TSL:5	n.20+2609A>G		intron	N/A
	ENSG00000290606	ENST00000716069.1		n.64-4871A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51768 AN: 152000 Hom.: 10964 Cov.: 33

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.341 AC: 51862 AN: 152118 Hom.: 11003 Cov.: 33 AF XY: 0.338 AC XY: 25110 AN XY: 74370

African (AFR) AF: 0.607 AC: 25153 AN: 41472

American (AMR) AF: 0.287 AC: 4383 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3472

East Asian (EAS) AF: 0.212 AC: 1095 AN: 5168

South Asian (SAS) AF: 0.227 AC: 1096 AN: 4822

European-Finnish (FIN) AF: 0.225 AC: 2381 AN: 10594

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15493 AN: 67986

Other (OTH) AF: 0.343 AC: 723 AN: 2110

Alfa AF: 0.263 Hom.: 12019

Bravo AF: 0.357

Asia WGS AF: 0.304 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.75
DANN	Benign	0.53
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs10401833; hg19: chr19-29136582;