rs1395351

Variant names:

• chr13-70994994-A-G
• rs1395351

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.187 AC: 7755 AN: 41482

American (AMR) AF: 0.320 AC: 4875 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3468

East Asian (EAS) AF: 0.226 AC: 1166 AN: 5156

South Asian (SAS) AF: 0.335 AC: 1614 AN: 4818

European-Finnish (FIN) AF: 0.263 AC: 2781 AN: 10568

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19865 AN: 67962

Other (OTH) AF: 0.289 AC: 610 AN: 2112

Alfa AF: 0.269 Hom.: 1075

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
PhyloP100		3.3

Splicing

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

Other links and lift over

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