10-43054487-C-T

Variant names:

• chr10-43054487-C-T
• rs7078220

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 0.255 in 152,090 control chromosomes in the GnomAD database, including 5,990 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 0.26 (5990 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38764 AN: 151968 Hom.: 5973 Cov.: 33

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0927

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.255 AC: 38823 AN: 152090 Hom.: 5990 Cov.: 33 AF XY: 0.248 AC XY: 18454 AN XY: 74354

African (AFR) AF: 0.430 AC: 17855 AN: 41524

American (AMR) AF: 0.235 AC: 3592 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3466

East Asian (EAS) AF: 0.143 AC: 738 AN: 5148

South Asian (SAS) AF: 0.0949 AC: 455 AN: 4794

European-Finnish (FIN) AF: 0.116 AC: 1224 AN: 10584

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13422 AN: 67978

Other (OTH) AF: 0.261 AC: 553 AN: 2116

Alfa AF: 0.223 Hom.: 4947

Bravo AF: 0.274

Asia WGS AF: 0.164 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7078220; hg19: chr10-43549935;