chr19-39259282-A-C

Variant names:

• chr19-39259282-A-C
• rs10424607

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 0.359 in 151,548 control chromosomes in the GnomAD database, including 10,678 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 0.36 (10678 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54281 AN: 151430 Hom.: 10648 Cov.: 29

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.359 AC: 54361 AN: 151548 Hom.: 10678 Cov.: 29 AF XY: 0.351 AC XY: 25987 AN XY: 74046

African (AFR) AF: 0.517 AC: 21314 AN: 41236

American (AMR) AF: 0.388 AC: 5906 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1181 AN: 3466

East Asian (EAS) AF: 0.209 AC: 1072 AN: 5132

South Asian (SAS) AF: 0.287 AC: 1373 AN: 4784

European-Finnish (FIN) AF: 0.196 AC: 2064 AN: 10504

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20261 AN: 67914

Other (OTH) AF: 0.353 AC: 736 AN: 2086

Alfa AF: 0.342 Hom.: 1192

Bravo AF: 0.383

Asia WGS AF: 0.273 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.36
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs10424607; hg19: chr19-39749922;