19-10505627-T-G

Variant names:

• chr19-10505627-T-G
• rs11668429

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 0.449 in 151,728 control chromosomes in the GnomAD database, including 17,224 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 0.45 (17224 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68039 AN: 151618 Hom.: 17186 Cov.: 31

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.449 AC: 68135 AN: 151728 Hom.: 17224 Cov.: 31 AF XY: 0.449 AC XY: 33274 AN XY: 74086

African (AFR) AF: 0.686 AC: 28410 AN: 41434

American (AMR) AF: 0.330 AC: 5026 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1298 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2663 AN: 5154

South Asian (SAS) AF: 0.426 AC: 2053 AN: 4816

European-Finnish (FIN) AF: 0.409 AC: 4276 AN: 10460

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23025 AN: 67868

Other (OTH) AF: 0.435 AC: 915 AN: 2102

Alfa AF: 0.376 Hom.: 37520

Bravo AF: 0.455

Asia WGS AF: 0.480 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.45
DANN	Benign	0.43
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs11668429; hg19: chr19-10616303;