rs1319868

chr15-98643750-G-T

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 0.172 in 152,134 control chromosomes in the GnomAD database, including 3,211 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 0.17 (3211 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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: 0.171 AC: 26064 AN: 152016 Hom.: 3199 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0898

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.172 AC: 26114 AN: 152134 Hom.: 3211 Cov.: 32 AF XY: 0.165 AC XY: 12237 AN XY: 74382

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0899

Gnomad4 FIN AF: 0.0316

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.153

Alfa AF: 0.131 Hom.: 1988

Bravo AF: 0.188

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	9.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1319868; hg19: chr15-99186979;