rs13207315

Variant names:

• chr6-31273350-T-C
• rs13207315

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 0.132 in 151,860 control chromosomes in the GnomAD database, including 1,491 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 0.13 (1491 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.231 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: 0.132 AC: 20045 AN: 151742 Hom.: 1489 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.132 AC: 20054 AN: 151860 Hom.: 1491 Cov.: 31 AF XY: 0.134 AC XY: 9946 AN XY: 74232

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.137

Alfa AF: 0.133 Hom.: 139

Bravo AF: 0.129

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.4
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13207315; hg19: chr6-31241127;