rs4263048

Variant names:

• chr19-53274077-G-A
• rs4263048

Your query was ambiguous. Multiple possible variants found:

• chr19-53274077-G-A
• chr19-53274077-G-T

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 0.194 in 152,086 control chromosomes in the GnomAD database, including 2,971 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 0.19 (2971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 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: 0.194 AC: 29485 AN: 151968 Hom.: 2965 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.194 AC: 29508 AN: 152086 Hom.: 2971 Cov.: 32 AF XY: 0.200 AC XY: 14850 AN XY: 74330

African (AFR) AF: 0.202 AC: 8387 AN: 41506

American (AMR) AF: 0.196 AC: 2997 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3470

East Asian (EAS) AF: 0.285 AC: 1471 AN: 5166

South Asian (SAS) AF: 0.320 AC: 1543 AN: 4820

European-Finnish (FIN) AF: 0.209 AC: 2209 AN: 10556

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11601 AN: 67978

Other (OTH) AF: 0.189 AC: 400 AN: 2114

Alfa AF: 0.176 Hom.: 7437

Bravo AF: 0.192

Asia WGS AF: 0.308 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.26
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs4263048; hg19: chr19-53777330;