rs2895795

Variant names:

• chr5-148825403-T-A
• rs2895795

Your query was ambiguous. Multiple possible variants found:

• chr5-148825403-T-A
• chr5-148825403-T-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 0.251 in 152,148 control chromosomes in the GnomAD database, including 5,252 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 0.25 (5252 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 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: 0.251 AC: 38170 AN: 152028 Hom.: 5248 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.263

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.251 AC: 38195 AN: 152148 Hom.: 5252 Cov.: 32 AF XY: 0.252 AC XY: 18736 AN XY: 74378

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.261

Alfa AF: 0.107 Hom.: 178

Bravo AF: 0.265

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.3
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2895795; hg19: chr5-148204966;