19-38780384-A-G

Variant names:

• chr19-38780384-A-G
• rs11671165

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 0.197 in 152,106 control chromosomes in the GnomAD database, including 3,599 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 0.20 (3599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569

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 (EAS) allele frequency at 95% confidence interval = 0.495 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: 0.197 AC: 29916 AN: 151988 Hom.: 3592 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.197 AC: 29936 AN: 152106 Hom.: 3599 Cov.: 32 AF XY: 0.201 AC XY: 14947 AN XY: 74360

African (AFR) AF: 0.0963 AC: 3998 AN: 41522

American (AMR) AF: 0.200 AC: 3057 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3468

East Asian (EAS) AF: 0.511 AC: 2639 AN: 5166

South Asian (SAS) AF: 0.374 AC: 1801 AN: 4816

European-Finnish (FIN) AF: 0.199 AC: 2110 AN: 10590

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14610 AN: 67980

Other (OTH) AF: 0.232 AC: 488 AN: 2106

Alfa AF: 0.189 Hom.: 390

Bravo AF: 0.189

Asia WGS AF: 0.437 AC: 1516 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	2.1
DANN	Benign	0.53
PhyloP100		-0.57

Splicing

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

Publications

Loading publications...

Other links and lift over

dbSNP: rs11671165; hg19: chr19-39271024;