19-7658575-C-T

Position:

• chr19-7658575-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.297 in 152,096 control chromosomes in the GnomAD database, including 7,042 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 0.30 (7042 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.7658575C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45139 AN: 151978 Hom.: 7035 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.297 AC: 45169 AN: 152096 Hom.: 7042 Cov.: 32 AF XY: 0.301 AC XY: 22402 AN XY: 74326

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.301

Alfa AF: 0.298 Hom.: 6843

Bravo AF: 0.302

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2081075; hg19: chr19-7723461;