rs13203464

Variant names:

• chr6-84908832-T-A
• rs13203464

Your query was ambiguous. Multiple possible variants found:

• chr6-84908832-T-A
• chr6-84908832-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0169 in 151,166 control chromosomes in the GnomAD database, including 33 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 0.017 (33 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.868
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0169 (2554/151166) while in subpopulation AMR AF = 0.0275 (415/15074). AF 95% confidence interval is 0.0253. There are 33 homozygotes in GnomAd4. There are 1223 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 33 gene

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: 0.0169 AC: 2554 AN: 151056 Hom.: 34 Cov.: 32

Gnomad AFR AF: 0.00570

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.0306

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000416

Gnomad FIN AF: 0.00824

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0243

Gnomad OTH AF: 0.0279

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

GnomAD4 genome AF: 0.0169 AC: 2554 AN: 151166 Hom.: 33 Cov.: 32 AF XY: 0.0166 AC XY: 1223 AN XY: 73844

African (AFR) AF: 0.00568 AC: 235 AN: 41376

American (AMR) AF: 0.0275 AC: 415 AN: 15074

Ashkenazi Jewish (ASJ) AF: 0.0306 AC: 106 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5162

South Asian (SAS) AF: 0.000624 AC: 3 AN: 4804

European-Finnish (FIN) AF: 0.00824 AC: 84 AN: 10196

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0243 AC: 1647 AN: 67788

Other (OTH) AF: 0.0276 AC: 58 AN: 2098

Alfa AF: 0.00720 Hom.: 1

Bravo AF: 0.0178

Asia WGS AF: 0.00174 AC: 6 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.51
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs13203464; hg19: chr6-85618550;