rs222054

Variant names:

• chr4-71738582-C-G
• rs222054

Your query was ambiguous. Multiple possible variants found:

• chr4-71738582-C-G
• chr4-71738582-C-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 0.268 in 152,002 control chromosomes in the GnomAD database, including 5,749 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 0.27 (5749 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 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: 0.268 AC: 40761 AN: 151884 Hom.: 5754 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.268 AC: 40774 AN: 152002 Hom.: 5749 Cov.: 32 AF XY: 0.274 AC XY: 20340 AN XY: 74290

African (AFR) AF: 0.191 AC: 7929 AN: 41462

American (AMR) AF: 0.233 AC: 3549 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 869 AN: 3470

East Asian (EAS) AF: 0.276 AC: 1420 AN: 5148

South Asian (SAS) AF: 0.412 AC: 1980 AN: 4808

European-Finnish (FIN) AF: 0.398 AC: 4205 AN: 10568

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.295 AC: 20025 AN: 67966

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.169 Hom.: 364

Bravo AF: 0.250

Asia WGS AF: 0.295 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.47
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs222054; hg19: chr4-72604299;