chr4-10200950-C-T

Variant names:

• chr4-10200950-C-T
• rs2868416

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 0.628 in 151,970 control chromosomes in the GnomAD database, including 30,570 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 0.63 (30570 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.68 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: 0.628 AC: 95424 AN: 151854 Hom.: 30540 Cov.: 33

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.628 AC: 95499 AN: 151970 Hom.: 30570 Cov.: 33 AF XY: 0.629 AC XY: 46700 AN XY: 74258

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.615

Alfa AF: 0.614 Hom.: 3521

Bravo AF: 0.614

Asia WGS AF: 0.631 AC: 2193 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2868416; hg19: chr4-10202574;