13-69421685-T-C

Variant names:

• chr13-69421685-T-C
• rs949627

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 0.366 in 152,134 control chromosomes in the GnomAD database, including 10,479 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 0.37 (10479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• 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 (EAS) allele frequency at 95% confidence interval = 0.437 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: 0.366 AC: 55665 AN: 152014 Hom.: 10467 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.366 AC: 55710 AN: 152134 Hom.: 10479 Cov.: 32 AF XY: 0.363 AC XY: 26999 AN XY: 74372

African (AFR) AF: 0.292 AC: 12134 AN: 41502

American (AMR) AF: 0.421 AC: 6442 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1352 AN: 3464

East Asian (EAS) AF: 0.453 AC: 2340 AN: 5170

South Asian (SAS) AF: 0.415 AC: 2006 AN: 4828

European-Finnish (FIN) AF: 0.352 AC: 3722 AN: 10584

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26609 AN: 67984

Other (OTH) AF: 0.385 AC: 814 AN: 2112

Alfa AF: 0.305 Hom.: 1130

Bravo AF: 0.368

Asia WGS AF: 0.462 AC: 1600 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.79
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs949627; hg19: chr13-69995817; COSMIC: COSV69361711;