rs1556775

Variant names:

• chr13-85667653-A-C
• rs1556775

Your query was ambiguous. Multiple possible variants found:

• chr13-85667653-A-C
• chr13-85667653-A-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.119 AC: 4938 AN: 41544

American (AMR) AF: 0.0383 AC: 585 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3472

East Asian (EAS) AF: 0.0160 AC: 83 AN: 5176

South Asian (SAS) AF: 0.0820 AC: 396 AN: 4830

European-Finnish (FIN) AF: 0.00659 AC: 70 AN: 10626

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0258 AC: 1751 AN: 67996

Other (OTH) AF: 0.0530 AC: 112 AN: 2112

Alfa AF: 0.0395 Hom.: 94

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
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1556775; hg19: chr13-86241788;