13-73317600-C-T

Variant names:

• chr13-73317600-C-T
• rs1411327

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 0.416 in 151,876 control chromosomes in the GnomAD database, including 13,478 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 0.42 (13478 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 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: 0.416 AC: 63155 AN: 151758 Hom.: 13459 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.416 AC: 63214 AN: 151876 Hom.: 13478 Cov.: 32 AF XY: 0.413 AC XY: 30640 AN XY: 74200

African (AFR) AF: 0.527 AC: 21837 AN: 41440

American (AMR) AF: 0.366 AC: 5575 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3464

East Asian (EAS) AF: 0.480 AC: 2472 AN: 5154

South Asian (SAS) AF: 0.310 AC: 1489 AN: 4804

European-Finnish (FIN) AF: 0.351 AC: 3684 AN: 10510

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25371 AN: 67950

Other (OTH) AF: 0.402 AC: 846 AN: 2104

Alfa AF: 0.382 Hom.: 6562

Bravo AF: 0.423

Asia WGS AF: 0.379 AC: 1318 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.81
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs1411327; hg19: chr13-73891737;