chr13-69421685-T-C

Variant names:

• chr13-69421685-T-C
• rs949627

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.385

Alfa AF: 0.304 Hom.: 1089

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

Splicing

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

Publications

LitVar

Other links and lift over

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