rs222054

Positions:

• chr4-71738582-C-G
• chr4-71738582-C-T

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 0.268 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.258

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs222054; hg19: chr4-72604299;