rs735273

Positions:

• chr19-19274602-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 0.419 in 151,924 control chromosomes in the GnomAD database, including 14,731 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 0.42 (14731 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 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: 0.418 AC: 63461 AN: 151806 Hom.: 14671 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.419 AC: 63588 AN: 151924 Hom.: 14731 Cov.: 31 AF XY: 0.415 AC XY: 30808 AN XY: 74252

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.415

Alfa AF: 0.358 Hom.: 5899

Bravo AF: 0.439

Asia WGS AF: 0.445 AC: 1547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs735273; hg19: chr19-19385411;