chr19-31675940-T-G

Position:

• chr19-31675940-T-G

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 0.175 in 152,092 control chromosomes in the GnomAD database, including 2,637 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 0.18 (2637 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 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: 0.175 AC: 26576 AN: 151974 Hom.: 2614 Cov.: 30

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.0981

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.175 AC: 26640 AN: 152092 Hom.: 2637 Cov.: 30 AF XY: 0.172 AC XY: 12805 AN XY: 74348

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0568

Gnomad4 EAS AF: 0.0983

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.138

Alfa AF: 0.157 Hom.: 907

Bravo AF: 0.178

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8104309; hg19: chr19-32166846;