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
• Publications: 8 publications found

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

African (AFR) AF: 0.0650 AC: 2700 AN: 41536

American (AMR) AF: 0.245 AC: 3743 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3468

East Asian (EAS) AF: 0.150 AC: 776 AN: 5162

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4820

European-Finnish (FIN) AF: 0.271 AC: 2876 AN: 10596

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 16006 AN: 67976

Other (OTH) AF: 0.212 AC: 447 AN: 2112

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
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs10448143; hg19: chr8-145673384;