rs13210554

Variant names:

• chr6-46736602-C-T
• rs13210554

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 0.201 in 152,170 control chromosomes in the GnomAD database, including 3,449 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 0.20 (3449 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 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: 0.201 AC: 30560 AN: 152052 Hom.: 3440 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.201 AC: 30594 AN: 152170 Hom.: 3449 Cov.: 33 AF XY: 0.208 AC XY: 15473 AN XY: 74380

African (AFR) AF: 0.127 AC: 5279 AN: 41526

American (AMR) AF: 0.288 AC: 4403 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 979 AN: 3464

East Asian (EAS) AF: 0.164 AC: 848 AN: 5186

South Asian (SAS) AF: 0.456 AC: 2192 AN: 4808

European-Finnish (FIN) AF: 0.228 AC: 2410 AN: 10576

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13772 AN: 68008

Other (OTH) AF: 0.217 AC: 458 AN: 2106

Alfa AF: 0.202 Hom.: 421

Bravo AF: 0.193

Asia WGS AF: 0.321 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs13210554; hg19: chr6-46704339;