rs7259265

Variant names:

• chr19-40659347-T-G
• rs7259265

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 0.198 in 152,110 control chromosomes in the GnomAD database, including 3,644 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 0.20 (3644 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 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: 0.198 AC: 30031 AN: 151992 Hom.: 3642 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.198 AC: 30063 AN: 152110 Hom.: 3644 Cov.: 32 AF XY: 0.195 AC XY: 14531 AN XY: 74354

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.175

Alfa AF: 0.157 Hom.: 2696

Bravo AF: 0.203

Asia WGS AF: 0.213 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7259265; hg19: chr19-41165252;