rs3814892

Variant names:

• chr19-638853-G-A
• rs3814892

Your query was ambiguous. Multiple possible variants found:

• chr19-638853-G-A
• chr19-638853-G-C

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 0.17 in 152,182 control chromosomes in the GnomAD database, including 2,566 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 0.17 (2566 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 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: 0.170 AC: 25918 AN: 152060 Hom.: 2565 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.170 AC: 25930 AN: 152182 Hom.: 2566 Cov.: 33 AF XY: 0.171 AC XY: 12748 AN XY: 74386

African (AFR) AF: 0.249 AC: 10348 AN: 41504

American (AMR) AF: 0.124 AC: 1896 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3468

East Asian (EAS) AF: 0.306 AC: 1577 AN: 5150

South Asian (SAS) AF: 0.270 AC: 1303 AN: 4824

European-Finnish (FIN) AF: 0.113 AC: 1200 AN: 10612

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8609 AN: 68004

Other (OTH) AF: 0.171 AC: 362 AN: 2114

Alfa AF: 0.141 Hom.: 3250

Bravo AF: 0.173

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.89
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs3814892; hg19: chr19-638853;