13-35764780-T-C

Variant names:

• chr13-35764780-T-C
• rs872060

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 0.219 in 151,936 control chromosomes in the GnomAD database, including 4,260 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 0.22 (4260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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: 0.219 AC: 33217 AN: 151820 Hom.: 4254 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.219 AC: 33251 AN: 151936 Hom.: 4260 Cov.: 32 AF XY: 0.221 AC XY: 16395 AN XY: 74242

African (AFR) AF: 0.313 AC: 12959 AN: 41376

American (AMR) AF: 0.170 AC: 2603 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 814 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2403 AN: 5122

South Asian (SAS) AF: 0.240 AC: 1159 AN: 4826

European-Finnish (FIN) AF: 0.159 AC: 1679 AN: 10584

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11084 AN: 67962

Other (OTH) AF: 0.205 AC: 431 AN: 2102

Alfa AF: 0.191 Hom.: 428

Bravo AF: 0.225

Asia WGS AF: 0.340 AC: 1187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.60
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs872060; hg19: chr13-36338917;