rs1549318

Variant names:

• chr15-70816808-C-T
• rs1549318

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 0.555 in 151,646 control chromosomes in the GnomAD database, including 24,179 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 0.56 (24179 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.709 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: 0.555 AC: 84146 AN: 151530 Hom.: 24160 Cov.: 30

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.555 AC: 84206 AN: 151646 Hom.: 24179 Cov.: 30 AF XY: 0.554 AC XY: 41019 AN XY: 74062

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.601

Alfa AF: 0.604 Hom.: 63235

Bravo AF: 0.570

Asia WGS AF: 0.523 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1549318; hg19: chr15-71109147;