10-43298177-C-T

Variant names:

• chr10-43298177-C-T
• rs2503872

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 0.289 in 151,900 control chromosomes in the GnomAD database, including 6,708 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 0.29 (6708 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43843 AN: 151796 Hom.: 6704 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.289 AC: 43864 AN: 151900 Hom.: 6708 Cov.: 31 AF XY: 0.287 AC XY: 21281 AN XY: 74208

African (AFR) AF: 0.194 AC: 8031 AN: 41408

American (AMR) AF: 0.252 AC: 3848 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1273 AN: 3466

East Asian (EAS) AF: 0.309 AC: 1596 AN: 5162

South Asian (SAS) AF: 0.306 AC: 1472 AN: 4812

European-Finnish (FIN) AF: 0.293 AC: 3084 AN: 10534

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.345 AC: 23423 AN: 67938

Other (OTH) AF: 0.314 AC: 661 AN: 2104

Alfa AF: 0.324 Hom.: 36471

Bravo AF: 0.279

Asia WGS AF: 0.303 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.32
DANN	Benign	0.63
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs2503872; hg19: chr10-43793625;