19-40980072-G-A

Position:

• chr19-40980072-G-A

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 151,874 control chromosomes in the GnomAD database, including 7,637 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 (7637 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

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 (EAS) allele frequency at 95% confidence interval = 0.445 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: 45262 AN: 151756 Hom.: 7638 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.298 AC: 45278 AN: 151874 Hom.: 7637 Cov.: 31 AF XY: 0.305 AC XY: 22633 AN XY: 74224

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.303

Alfa AF: 0.205 Hom.: 507

Bravo AF: 0.288

Asia WGS AF: 0.374 AC: 1303 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	3.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4803413; hg19: chr19-41485977;