rs1556775

chr13-85667653-A-C

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 0.053 in 152,240 control chromosomes in the GnomAD database, including 364 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 0.053 (364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 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: 0.0530 AC: 8067 AN: 152122 Hom.: 363 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0383

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.00659

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0258

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0530 AC: 8074 AN: 152240 Hom.: 364 Cov.: 32 AF XY: 0.0511 AC XY: 3805 AN XY: 74440

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0383

Gnomad4 ASJ AF: 0.0228

Gnomad4 EAS AF: 0.0160

Gnomad4 SAS AF: 0.0820

Gnomad4 FIN AF: 0.00659

Gnomad4 NFE AF: 0.0258

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0359 Hom.: 65

Bravo AF: 0.0554

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.12
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1556775; hg19: chr13-86241788;