rs1395351

Positions:

• chr13-70994994-A-G

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 0.264 in 152,024 control chromosomes in the GnomAD database, including 5,521 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 0.26 (5521 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 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: 0.263 AC: 40023 AN: 151906 Hom.: 5511 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.264 AC: 40068 AN: 152024 Hom.: 5521 Cov.: 32 AF XY: 0.262 AC XY: 19499 AN XY: 74306

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.289

Alfa AF: 0.271 Hom.: 1069

Bravo AF: 0.263

Asia WGS AF: 0.286 AC: 996 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395351; hg19: chr13-71569126; COSMIC: COSV53409107;