rs769446

chr19-44905371-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 0.0708 in 149,116 control chromosomes in the GnomAD database, including 452 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 0.071 (452 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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 = 0.097 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0709 AC: 10561 AN: 148988 Hom.: 451 Cov.: 32

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0537

Gnomad ASJ AF: 0.0722

Gnomad EAS AF: 0.0932

Gnomad SAS AF: 0.0624

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0662

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.0771

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

GnomAD4 genome AF: 0.0708 AC: 10558 AN: 149116 Hom.: 452 Cov.: 32 AF XY: 0.0685 AC XY: 4988 AN XY: 72868

Gnomad4 AFR AF: 0.0359

Gnomad4 AMR AF: 0.0537

Gnomad4 ASJ AF: 0.0722

Gnomad4 EAS AF: 0.0930

Gnomad4 SAS AF: 0.0621

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0990

Gnomad4 OTH AF: 0.0788

Alfa AF: 0.0881 Hom.: 128

Bravo AF: 0.0686

Asia WGS AF: 0.0960 AC: 334 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.3
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs769446; hg19: chr19-45408628;