rs1330948

Variant names:

• chr13-106741883-T-C
• rs1330948

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 0.221 in 152,178 control chromosomes in the GnomAD database, including 3,981 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 (3981 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.258 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: 0.221 AC: 33540 AN: 152060 Hom.: 3977 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.221 AC: 33569 AN: 152178 Hom.: 3981 Cov.: 33 AF XY: 0.223 AC XY: 16585 AN XY: 74396

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.205

Alfa AF: 0.254 Hom.: 2415

Bravo AF: 0.204

Asia WGS AF: 0.194 AC: 671 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0080
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330948; hg19: chr13-107394231;