rs2391371

Variant names:

• chr1-94133728-T-A
• rs2391371

Your query was ambiguous. Multiple possible variants found:

• chr1-94133728-T-A
• chr1-94133728-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 0.0557 in 152,266 control chromosomes in the GnomAD database, including 341 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 0.056 (341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

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 = 0.125 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: 0.0557 AC: 8472 AN: 152148 Hom.: 340 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0650

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0439

Gnomad FIN AF: 0.0181

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0557 AC: 8488 AN: 152266 Hom.: 341 Cov.: 32 AF XY: 0.0558 AC XY: 4158 AN XY: 74458

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.0650

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0441

Gnomad4 FIN AF: 0.0181

Gnomad4 NFE AF: 0.0284

Gnomad4 OTH AF: 0.0644

Alfa AF: 0.0399 Hom.: 25

Bravo AF: 0.0616

Asia WGS AF: 0.0760 AC: 265 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	1.6
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2391371; hg19: chr1-94599284;