19-34687938-T-C

Position:

• chr19-34687938-T-C

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 0.298 in 152,072 control chromosomes in the GnomAD database, including 7,535 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 (7535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45315 AN: 151954 Hom.: 7540 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.298 AC: 45311 AN: 152072 Hom.: 7535 Cov.: 32 AF XY: 0.298 AC XY: 22172 AN XY: 74324

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.304

Alfa AF: 0.333 Hom.: 1116

Bravo AF: 0.281

Asia WGS AF: 0.262 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.7
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7249990; hg19: chr19-35178843;