4-10200950-C-T

Variant names:

• chr4-10200950-C-T
• rs2868416

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 0.628 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.533 AC: 22084 AN: 41450

American (AMR) AF: 0.612 AC: 9357 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2027 AN: 3468

East Asian (EAS) AF: 0.547 AC: 2819 AN: 5156

South Asian (SAS) AF: 0.678 AC: 3268 AN: 4822

European-Finnish (FIN) AF: 0.704 AC: 7395 AN: 10506

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.685 AC: 46567 AN: 67968

Other (OTH) AF: 0.615 AC: 1300 AN: 2114

Alfa AF: 0.609 Hom.: 4326

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
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs2868416; hg19: chr4-10202574;