chr1-21938093-A-G

Variant names:

• chr1-21938093-A-G
• rs4233280

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 0.936 in 147,052 control chromosomes in the GnomAD database, including 64,964 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 0.94 (64964 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.985 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: 0.936 AC: 137609 AN: 146976 Hom.: 64937 Cov.: 24

Gnomad AFR AF: 0.799

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.969

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.993

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.971

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.950

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

GnomAD4 genome AF: 0.936 AC: 137675 AN: 147052 Hom.: 64964 Cov.: 24 AF XY: 0.938 AC XY: 66879 AN XY: 71306

African (AFR) AF: 0.799 AC: 31061 AN: 38854

American (AMR) AF: 0.969 AC: 14239 AN: 14694

Ashkenazi Jewish (ASJ) AF: 0.983 AC: 3403 AN: 3462

East Asian (EAS) AF: 0.978 AC: 4891 AN: 5000

South Asian (SAS) AF: 0.993 AC: 4717 AN: 4750

European-Finnish (FIN) AF: 0.976 AC: 9039 AN: 9260

Middle Eastern (MID) AF: 0.969 AC: 277 AN: 286

European-Non Finnish (NFE) AF: 0.991 AC: 67192 AN: 67788

Other (OTH) AF: 0.950 AC: 1948 AN: 2050

Alfa AF: 0.976 Hom.: 34033

Bravo AF: 0.928

Asia WGS AF: 0.968 AC: 3357 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4233280; hg19: chr1-22264586;