19-14476080-G-T

Variant names:

• chr19-14476080-G-T
• rs3810254

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 0.138 in 151,954 control chromosomes in the GnomAD database, including 2,220 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 0.14 (2220 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 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: 0.138 AC: 20994 AN: 151836 Hom.: 2214 Cov.: 32

Gnomad AFR AF: 0.0641

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.138 AC: 21012 AN: 151954 Hom.: 2220 Cov.: 32 AF XY: 0.142 AC XY: 10565 AN XY: 74278

African (AFR) AF: 0.0640 AC: 2653 AN: 41434

American (AMR) AF: 0.171 AC: 2610 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 453 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3167 AN: 5154

South Asian (SAS) AF: 0.205 AC: 990 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1216 AN: 10586

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9425 AN: 67894

Other (OTH) AF: 0.143 AC: 301 AN: 2110

Alfa AF: 0.135 Hom.: 2152

Bravo AF: 0.142

Asia WGS AF: 0.389 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.39
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs3810254; hg19: chr19-14586892;