19-6406007-C-T

Variant names:

• chr19-6406007-C-T
• rs7259085
• ENST00000596254.1:n.204-5714C>T

Variant summary

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

The ENST00000596254.1(ENSG00000293438):​n.204-5714C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 150,030 control chromosomes in the GnomAD database, including 1,507 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 0.10 (1507 hom., cov: 32)
• Consequence: ENSG00000293438 ENST00000596254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 0 publications found

Genes affected

ENSG00000293438 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC390877	NR_172890.1	n.276-5714C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293438	ENST00000596254.1	n.204-5714C>T		intron_variant	Intron 1 of 2	1
ENSG00000293438	ENST00000593563.2	n.92-5714C>T		intron_variant	Intron 1 of 2	3
ENSG00000214347	ENST00000637688.2	n.365-5714C>T		intron_variant	Intron 3 of 4	6

Frequencies

GnomAD3 genomes AF: 0.0995 AC: 14915 AN: 149918 Hom.: 1511 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.00111

Gnomad AMR AF: 0.0561

Gnomad ASJ AF: 0.0541

Gnomad EAS AF: 0.00885

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0350

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.0264

Gnomad OTH AF: 0.0944

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

GnomAD4 genome AF: 0.0995 AC: 14928 AN: 150030 Hom.: 1507 Cov.: 32 AF XY: 0.0994 AC XY: 7268 AN XY: 73152

African (AFR) AF: 0.269 AC: 10988 AN: 40884

American (AMR) AF: 0.0560 AC: 842 AN: 15034

Ashkenazi Jewish (ASJ) AF: 0.0541 AC: 187 AN: 3456

East Asian (EAS) AF: 0.00907 AC: 45 AN: 4964

South Asian (SAS) AF: 0.107 AC: 501 AN: 4698

European-Finnish (FIN) AF: 0.0350 AC: 359 AN: 10256

Middle Eastern (MID) AF: 0.107 AC: 30 AN: 280

European-Non Finnish (NFE) AF: 0.0264 AC: 1781 AN: 67478

Other (OTH) AF: 0.0934 AC: 194 AN: 2076

Alfa AF: 0.0699 Hom.: 113

Bravo AF: 0.105

Asia WGS AF: 0.0660 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.86
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs7259085; hg19: chr19-6406018;