19-22873544-T-G

Variant names:

• chr19-22873544-T-G
• rs7246967

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.205 in 152,180 control chromosomes in the GnomAD database, including 3,756 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 0.20 (3756 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 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: 0.205 AC: 31148 AN: 152062 Hom.: 3748 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.205 AC: 31196 AN: 152180 Hom.: 3756 Cov.: 32 AF XY: 0.202 AC XY: 15010 AN XY: 74402

African (AFR) AF: 0.333 AC: 13837 AN: 41500

American (AMR) AF: 0.167 AC: 2556 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3472

East Asian (EAS) AF: 0.164 AC: 850 AN: 5170

South Asian (SAS) AF: 0.130 AC: 625 AN: 4826

European-Finnish (FIN) AF: 0.161 AC: 1708 AN: 10604

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10444 AN: 68000

Other (OTH) AF: 0.219 AC: 462 AN: 2112

Alfa AF: 0.152 Hom.: 758

Bravo AF: 0.213

Asia WGS AF: 0.185 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.8
DANN	Benign	0.39
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7246967; hg19: chr19-23056346;