rs10445672

Variant names:

• chr2-145347686-T-C
• rs10445672

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 0.216 in 151,608 control chromosomes in the GnomAD database, including 4,306 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 0.22 (4306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 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: 0.216 AC: 32739 AN: 151488 Hom.: 4287 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.216 AC: 32813 AN: 151608 Hom.: 4306 Cov.: 32 AF XY: 0.214 AC XY: 15827 AN XY: 74090

African (AFR) AF: 0.368 AC: 15241 AN: 41382

American (AMR) AF: 0.163 AC: 2466 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3464

East Asian (EAS) AF: 0.108 AC: 556 AN: 5138

South Asian (SAS) AF: 0.172 AC: 830 AN: 4820

European-Finnish (FIN) AF: 0.152 AC: 1611 AN: 10604

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10845 AN: 67744

Other (OTH) AF: 0.194 AC: 408 AN: 2100

Alfa AF: 0.175 Hom.: 9895

Bravo AF: 0.221

Asia WGS AF: 0.145 AC: 505 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.69
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10445672; hg19: chr2-146105254;