15-69157508-T-C

Variant names:

• chr15-69157508-T-C
• rs1553251

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 0.705 in 152,150 control chromosomes in the GnomAD database, including 37,941 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 0.71 (37941 hom., cov: 33)
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.744 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: 0.705 AC: 107196 AN: 152032 Hom.: 37900 Cov.: 33

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.705 AC: 107283 AN: 152150 Hom.: 37941 Cov.: 33 AF XY: 0.705 AC XY: 52418 AN XY: 74384

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.705

Alfa AF: 0.693 Hom.: 14278

Bravo AF: 0.713

Asia WGS AF: 0.645 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.8
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553251; hg19: chr15-69449847;