rs435309

Variant names:

• chr13-62286384-T-C
• rs435309

Your query was ambiguous. Multiple possible variants found:

• chr13-62286384-T-C
• chr13-62286384-T-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 0.484 in 151,290 control chromosomes in the GnomAD database, including 18,257 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 0.48 (18257 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.566 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: 0.484 AC: 73211 AN: 151168 Hom.: 18246 Cov.: 30

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.484 AC: 73242 AN: 151290 Hom.: 18257 Cov.: 30 AF XY: 0.476 AC XY: 35179 AN XY: 73880

African (AFR) AF: 0.372 AC: 15346 AN: 41288

American (AMR) AF: 0.506 AC: 7678 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1785 AN: 3464

East Asian (EAS) AF: 0.444 AC: 2267 AN: 5102

South Asian (SAS) AF: 0.403 AC: 1944 AN: 4820

European-Finnish (FIN) AF: 0.398 AC: 4165 AN: 10460

Middle Eastern (MID) AF: 0.552 AC: 160 AN: 290

European-Non Finnish (NFE) AF: 0.570 AC: 38610 AN: 67698

Other (OTH) AF: 0.503 AC: 1056 AN: 2100

Alfa AF: 0.379 Hom.: 1013

Bravo AF: 0.489

Asia WGS AF: 0.437 AC: 1520 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	2.0
DANN	Benign	0.72
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs435309; hg19: chr13-62860517;