rs10445672

Variant names:

• chr2-145347686-T-C
• rs10445672

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.216 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

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.194

Alfa AF: 0.165 Hom.: 4123

Bravo AF: 0.221

Asia WGS AF: 0.145 AC: 505 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
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: rs10445672; hg19: chr2-146105254;