19-40953336-T-C

Variant names:

• chr19-40953336-T-C
• rs3889806

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 0.739 in 152,064 control chromosomes in the GnomAD database, including 42,576 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 0.74 (42576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112261 AN: 151946 Hom.: 42536 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.834

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.739 AC: 112357 AN: 152064 Hom.: 42576 Cov.: 32 AF XY: 0.743 AC XY: 55236 AN XY: 74324

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.743

Alfa AF: 0.664 Hom.: 38574

Bravo AF: 0.752

Asia WGS AF: 0.772 AC: 2683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3889806; hg19: chr19-41459241;