rs2147995

Variant names:

• chr13-23951465-A-C
• rs2147995

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;