chr19-2953811-G-A

Variant names:

• chr19-2953811-G-A
• rs11666694

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 0.252 in 152,042 control chromosomes in the GnomAD database, including 6,106 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 0.25 (6106 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 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: 0.252 AC: 38305 AN: 151924 Hom.: 6110 Cov.: 31

Gnomad AFR AF: 0.0615

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.252 AC: 38287 AN: 152042 Hom.: 6106 Cov.: 31 AF XY: 0.252 AC XY: 18749 AN XY: 74320

African (AFR) AF: 0.0613 AC: 2546 AN: 41524

American (AMR) AF: 0.231 AC: 3517 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1164 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1314 AN: 5154

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4818

European-Finnish (FIN) AF: 0.362 AC: 3823 AN: 10560

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23339 AN: 67948

Other (OTH) AF: 0.268 AC: 567 AN: 2112

Alfa AF: 0.315 Hom.: 4849

Bravo AF: 0.234

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.26
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs11666694; hg19: chr19-2953809; COSMIC: COSV53435600;