rs2147995

Positions:

• chr13-23951465-A-C
• chr13-23951465-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 0.181 in 152,120 control chromosomes in the GnomAD database, including 3,100 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 0.18 (3100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27554 AN: 152002 Hom.: 3091 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.0883

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.181 AC: 27587 AN: 152120 Hom.: 3100 Cov.: 32 AF XY: 0.185 AC XY: 13783 AN XY: 74366

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.0883

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.209

Alfa AF: 0.184 Hom.: 2916

Bravo AF: 0.200

Asia WGS AF: 0.266 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.86
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2147995; hg19: chr13-24525604;