chr15-97916486-G-A

Position:

• chr15-97916486-G-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 0.0912 in 152,138 control chromosomes in the GnomAD database, including 1,216 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 0.091 (1216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 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: 0.0911 AC: 13850 AN: 152020 Hom.: 1215 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.0572

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0412

Gnomad OTH AF: 0.0685

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

GnomAD4 genome AF: 0.0912 AC: 13876 AN: 152138 Hom.: 1216 Cov.: 32 AF XY: 0.0879 AC XY: 6540 AN XY: 74366

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.0420

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.00484

Gnomad4 SAS AF: 0.0570

Gnomad4 FIN AF: 0.0268

Gnomad4 NFE AF: 0.0412

Gnomad4 OTH AF: 0.0678

Alfa AF: 0.0418 Hom.: 243

Bravo AF: 0.0986

Asia WGS AF: 0.0490 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7163331; hg19: chr15-98459716;