rs11635084

Positions:

• chr15-78394481-A-G
• chr15-78394481-A-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 0.485 in 151,962 control chromosomes in the GnomAD database, including 19,394 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 0.49 (19394 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 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: 0.485 AC: 73636 AN: 151844 Hom.: 19362 Cov.: 31

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.485 AC: 73709 AN: 151962 Hom.: 19394 Cov.: 31 AF XY: 0.486 AC XY: 36122 AN XY: 74256

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.453

Alfa AF: 0.399 Hom.: 24335

Bravo AF: 0.493

Asia WGS AF: 0.508 AC: 1764 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	0.98
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11635084; hg19: chr15-78686823;