rs7247032

Positions:

• chr19-57068415-A-C
• chr19-57068415-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.469 in 151,916 control chromosomes in the GnomAD database, including 18,206 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 0.47 (18206 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71113 AN: 151798 Hom.: 18147 Cov.: 31

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.469 AC: 71237 AN: 151916 Hom.: 18206 Cov.: 31 AF XY: 0.468 AC XY: 34772 AN XY: 74238

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.453

Alfa AF: 0.389 Hom.: 15537

Bravo AF: 0.486

Asia WGS AF: 0.479 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7247032; hg19: chr19-57579783;