rs10448143

Variant names:

• chr8-144448001-C-T
• rs10448143

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 0.187 in 152,170 control chromosomes in the GnomAD database, including 3,185 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 0.19 (3185 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.238 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: 0.187 AC: 28418 AN: 152052 Hom.: 3189 Cov.: 33

Gnomad AFR AF: 0.0651

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.187 AC: 28423 AN: 152170 Hom.: 3185 Cov.: 33 AF XY: 0.189 AC XY: 14062 AN XY: 74376

Gnomad4 AFR AF: 0.0650 AC: 0.0650039 AN: 0.0650039

Gnomad4 AMR AF: 0.245 AC: 0.244736 AN: 0.244736

Gnomad4 ASJ AF: 0.201 AC: 0.201269 AN: 0.201269

Gnomad4 EAS AF: 0.150 AC: 0.150329 AN: 0.150329

Gnomad4 SAS AF: 0.210 AC: 0.209959 AN: 0.209959

Gnomad4 FIN AF: 0.271 AC: 0.271423 AN: 0.271423

Gnomad4 NFE AF: 0.235 AC: 0.235465 AN: 0.235465

Gnomad4 OTH AF: 0.212 AC: 0.211648 AN: 0.211648

Alfa AF: 0.200 Hom.: 2837

Bravo AF: 0.179

Asia WGS AF: 0.179 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10448143; hg19: chr8-145673384;