rs7245959

Variant names:

• chr19-30888202-T-C
• rs7245959

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 0.392 in 152,068 control chromosomes in the GnomAD database, including 12,317 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 0.39 (12317 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.595 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: 0.393 AC: 59642 AN: 151950 Hom.: 12306 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.392 AC: 59670 AN: 152068 Hom.: 12317 Cov.: 32 AF XY: 0.399 AC XY: 29630 AN XY: 74318

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.443

Alfa AF: 0.391 Hom.: 2816

Bravo AF: 0.383

Asia WGS AF: 0.545 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
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: rs7245959; hg19: chr19-31379109;