chr19-4077098-A-C

Variant names:

• chr19-4077098-A-C
• rs7251928

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 0.369 in 151,938 control chromosomes in the GnomAD database, including 15,662 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 0.37 (15662 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55914 AN: 151820 Hom.: 15606 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0190

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.369 AC: 56022 AN: 151938 Hom.: 15662 Cov.: 31 AF XY: 0.361 AC XY: 26818 AN XY: 74278

African (AFR) AF: 0.793 AC: 32857 AN: 41438

American (AMR) AF: 0.213 AC: 3247 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 744 AN: 3462

East Asian (EAS) AF: 0.0188 AC: 97 AN: 5148

South Asian (SAS) AF: 0.201 AC: 970 AN: 4816

European-Finnish (FIN) AF: 0.214 AC: 2260 AN: 10566

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.220 AC: 14939 AN: 67944

Other (OTH) AF: 0.336 AC: 709 AN: 2110

Alfa AF: 0.282 Hom.: 18143

Bravo AF: 0.388

Asia WGS AF: 0.147 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.44
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7251928; hg19: chr19-4077096;