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. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.100 AC: 4165 AN: 41534

American (AMR) AF: 0.0650 AC: 994 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3472

East Asian (EAS) AF: 0.134 AC: 693 AN: 5184

South Asian (SAS) AF: 0.0441 AC: 213 AN: 4826

European-Finnish (FIN) AF: 0.0181 AC: 192 AN: 10614

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0284 AC: 1935 AN: 68026

Other (OTH) AF: 0.0644 AC: 136 AN: 2112

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
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs2391371; hg19: chr1-94599284;