rs13207315

chr6-31273350-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;