rs4388693

Variant names:

• chr1-231084618-G-A
• rs4388693

Your query was ambiguous. Multiple possible variants found:

• chr1-231084618-G-A
• chr1-231084618-G-C
• chr1-231084618-G-T

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 0.533 in 152,090 control chromosomes in the GnomAD database, including 23,084 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 0.53 (23084 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 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: 0.533 AC: 81019 AN: 151972 Hom.: 23064 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.533 AC: 81065 AN: 152090 Hom.: 23084 Cov.: 33 AF XY: 0.536 AC XY: 39881 AN XY: 74344

African (AFR) AF: 0.331 AC: 13720 AN: 41480

American (AMR) AF: 0.560 AC: 8556 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2107 AN: 3468

East Asian (EAS) AF: 0.869 AC: 4496 AN: 5176

South Asian (SAS) AF: 0.739 AC: 3564 AN: 4822

European-Finnish (FIN) AF: 0.566 AC: 5974 AN: 10556

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.598 AC: 40647 AN: 67982

Other (OTH) AF: 0.568 AC: 1199 AN: 2112

Alfa AF: 0.578 Hom.: 32388

Bravo AF: 0.525

Asia WGS AF: 0.759 AC: 2637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.9
DANN	Benign	0.48
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs4388693; hg19: chr1-231220364;