rs387504

Variant names:

• chr19-43941836-G-A
• rs387504

Your query was ambiguous. Multiple possible variants found:

• chr19-43941836-G-A
• chr19-43941836-G-C
• chr19-43941836-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 0.279 in 151,686 control chromosomes in the GnomAD database, including 6,626 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 0.28 (6626 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 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: 0.279 AC: 42345 AN: 151568 Hom.: 6618 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.279 AC: 42360 AN: 151686 Hom.: 6626 Cov.: 32 AF XY: 0.282 AC XY: 20888 AN XY: 74108

African (AFR) AF: 0.126 AC: 5205 AN: 41434

American (AMR) AF: 0.383 AC: 5833 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3466

East Asian (EAS) AF: 0.333 AC: 1714 AN: 5152

South Asian (SAS) AF: 0.262 AC: 1260 AN: 4812

European-Finnish (FIN) AF: 0.306 AC: 3210 AN: 10474

Middle Eastern (MID) AF: 0.399 AC: 114 AN: 286

European-Non Finnish (NFE) AF: 0.334 AC: 22669 AN: 67802

Other (OTH) AF: 0.318 AC: 673 AN: 2116

Alfa AF: 0.307 Hom.: 941

Bravo AF: 0.280

Asia WGS AF: 0.268 AC: 930 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.26
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs387504; hg19: chr19-44445988;