rs619819

Variant names:

• chr4-129454790-G-C
• rs619819

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 0.327 in 152,000 control chromosomes in the GnomAD database, including 8,343 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 0.33 (8343 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 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: 0.327 AC: 49631 AN: 151882 Hom.: 8328 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.327 AC: 49678 AN: 152000 Hom.: 8343 Cov.: 32 AF XY: 0.325 AC XY: 24108 AN XY: 74286

African (AFR) AF: 0.282 AC: 11701 AN: 41464

American (AMR) AF: 0.303 AC: 4621 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1314 AN: 3472

East Asian (EAS) AF: 0.266 AC: 1375 AN: 5178

South Asian (SAS) AF: 0.211 AC: 1014 AN: 4812

European-Finnish (FIN) AF: 0.365 AC: 3848 AN: 10556

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24547 AN: 67950

Other (OTH) AF: 0.302 AC: 638 AN: 2114

Alfa AF: 0.355 Hom.: 1196

Bravo AF: 0.320

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.69
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs619819; hg19: chr4-130375945; COSMIC: COSV66933067;