rs4075205

Variant names:

• chr8-143203248-T-C
• rs4075205

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 0.402 in 152,110 control chromosomes in the GnomAD database, including 12,613 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 0.40 (12613 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 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: 0.402 AC: 61087 AN: 151992 Hom.: 12601 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.402 AC: 61121 AN: 152110 Hom.: 12613 Cov.: 33 AF XY: 0.396 AC XY: 29436 AN XY: 74338

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.418

Alfa AF: 0.439 Hom.: 14033

Bravo AF: 0.405

Asia WGS AF: 0.319 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.9
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4075205; hg19: chr8-144284709;