rs10485945

Variant names:

• chr7-49274192-C-T
• rs10485945

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 0.0932 in 152,146 control chromosomes in the GnomAD database, including 744 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 0.093 (744 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.68
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 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: 0.0931 AC: 14159 AN: 152028 Hom.: 744 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.0780

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

GnomAD4 genome AF: 0.0932 AC: 14181 AN: 152146 Hom.: 744 Cov.: 33 AF XY: 0.0958 AC XY: 7120 AN XY: 74344

African (AFR) AF: 0.124 AC: 5136 AN: 41516

American (AMR) AF: 0.0459 AC: 701 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0282 AC: 98 AN: 3470

East Asian (EAS) AF: 0.170 AC: 876 AN: 5162

South Asian (SAS) AF: 0.0987 AC: 476 AN: 4824

European-Finnish (FIN) AF: 0.147 AC: 1558 AN: 10570

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0757 AC: 5150 AN: 68010

Other (OTH) AF: 0.0795 AC: 168 AN: 2112

Alfa AF: 0.0848 Hom.: 109

Bravo AF: 0.0865

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0060
DANN	Benign	0.69
PhyloP100		-4.7

Splicing

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

Other links and lift over

dbSNP: rs10485945; hg19: chr7-49313788;