rs4233508

Variant names:

• chr1-39952892-T-C
• rs4233508

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 0.272 in 151,998 control chromosomes in the GnomAD database, including 6,488 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 (6488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.89
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 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: 0.273 AC: 41406 AN: 151880 Hom.: 6483 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.272 AC: 41419 AN: 151998 Hom.: 6488 Cov.: 32 AF XY: 0.278 AC XY: 20618 AN XY: 74280

African (AFR) AF: 0.115 AC: 4751 AN: 41478

American (AMR) AF: 0.361 AC: 5503 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3470

East Asian (EAS) AF: 0.499 AC: 2578 AN: 5166

South Asian (SAS) AF: 0.471 AC: 2261 AN: 4804

European-Finnish (FIN) AF: 0.289 AC: 3057 AN: 10564

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.313 AC: 21299 AN: 67944

Other (OTH) AF: 0.293 AC: 618 AN: 2106

Alfa AF: 0.292 Hom.: 3204

Bravo AF: 0.265

Asia WGS AF: 0.426 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	18
DANN	Benign	0.87
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs4233508; hg19: chr1-40418564;