rs74676832

Variant names:

• chr19-56171378-T-A
• rs74676832

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 0.0425 in 152,278 control chromosomes in the GnomAD database, including 157 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 0.042 (157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0657 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: 0.0423 AC: 6433 AN: 152160 Hom.: 152 Cov.: 32

Gnomad AFR AF: 0.0673

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0278

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0178

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0394

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0425 AC: 6465 AN: 152278 Hom.: 157 Cov.: 32 AF XY: 0.0409 AC XY: 3045 AN XY: 74466

African (AFR) AF: 0.0678 AC: 2818 AN: 41548

American (AMR) AF: 0.0277 AC: 424 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00750 AC: 26 AN: 3468

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5192

South Asian (SAS) AF: 0.0387 AC: 187 AN: 4830

European-Finnish (FIN) AF: 0.0178 AC: 189 AN: 10606

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0394 AC: 2680 AN: 68024

Other (OTH) AF: 0.0289 AC: 61 AN: 2112

Alfa AF: 0.0434 Hom.: 21

Bravo AF: 0.0433

Asia WGS AF: 0.0440 AC: 153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.51
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs74676832; hg19: chr19-56682747;