rs7259340

chr19-43682501-C-A

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 0.295 in 149,792 control chromosomes in the GnomAD database, including 6,871 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 0.29 (6871 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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 (NFE) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44189 AN: 149722 Hom.: 6877 Cov.: 29

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.400

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.295 AC: 44175 AN: 149792 Hom.: 6871 Cov.: 29 AF XY: 0.287 AC XY: 21012 AN XY: 73102

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.0461

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.307

Alfa AF: 0.310 Hom.: 1786

Bravo AF: 0.291

Asia WGS AF: 0.172 AC: 597 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.24
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7259340; hg19: chr19-44186653;