rs2391371

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;