19-22372052-T-C

Variant names:

• chr19-22372052-T-C
• rs1865075

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 0.574 in 151,936 control chromosomes in the GnomAD database, including 25,260 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 0.57 (25260 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.737 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: 0.574 AC: 87091 AN: 151818 Hom.: 25220 Cov.: 31

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.574 AC: 87189 AN: 151936 Hom.: 25260 Cov.: 31 AF XY: 0.581 AC XY: 43135 AN XY: 74262

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.590

Alfa AF: 0.561 Hom.: 11216

Bravo AF: 0.568

Asia WGS AF: 0.719 AC: 2499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1865075; hg19: chr19-22554854;