chr19-49043554-T-C

Variant names:

• chr19-49043554-T-C
• rs4801789

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 0.353 in 120,728 control chromosomes in the GnomAD database, including 5,484 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 0.35 (5484 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.414 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: 0.353 AC: 42612 AN: 120626 Hom.: 5477 Cov.: 33

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.353 AC: 42648 AN: 120728 Hom.: 5484 Cov.: 33 AF XY: 0.353 AC XY: 20756 AN XY: 58804

African (AFR) AF: 0.394 AC: 13025 AN: 33026

American (AMR) AF: 0.424 AC: 5159 AN: 12180

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1144 AN: 2954

East Asian (EAS) AF: 0.181 AC: 783 AN: 4316

South Asian (SAS) AF: 0.366 AC: 1450 AN: 3966

European-Finnish (FIN) AF: 0.255 AC: 1936 AN: 7596

Middle Eastern (MID) AF: 0.298 AC: 62 AN: 208

European-Non Finnish (NFE) AF: 0.338 AC: 18257 AN: 54070

Other (OTH) AF: 0.353 AC: 600 AN: 1702

Alfa AF: 0.339 Hom.: 564

Asia WGS AF: 0.302 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.14
PhyloP100		-0.82
PromoterAI		0.047	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4801789; hg19: chr19-49546811; COSMIC: COSV56823433;