chr10-73949409-T-TTTTA

Variant names:

• chr10-73949409-T-TTTTA
• rs3998225

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.012 (12 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0123 (1663/134932) while in subpopulation NFE AF = 0.0175 (1119/63796). AF 95% confidence interval is 0.0167. There are 12 homozygotes in GnomAd4. There are 729 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 12 gene

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: 0.0123 AC: 1665 AN: 134894 Hom.: 12 Cov.: 0

Gnomad AFR AF: 0.00430

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00949

Gnomad ASJ AF: 0.0178

Gnomad EAS AF: 0.00632

Gnomad SAS AF: 0.0113

Gnomad FIN AF: 0.0151

Gnomad MID AF: 0.0100

Gnomad NFE AF: 0.0176

Gnomad OTH AF: 0.0126

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

GnomAD4 genome AF: 0.0123 AC: 1663 AN: 134932 Hom.: 12 Cov.: 0 AF XY: 0.0113 AC XY: 729 AN XY: 64612

African (AFR) AF: 0.00429 AC: 155 AN: 36136

American (AMR) AF: 0.00948 AC: 124 AN: 13076

Ashkenazi Jewish (ASJ) AF: 0.0178 AC: 59 AN: 3314

East Asian (EAS) AF: 0.00633 AC: 29 AN: 4578

South Asian (SAS) AF: 0.0111 AC: 45 AN: 4066

European-Finnish (FIN) AF: 0.0151 AC: 107 AN: 7088

Middle Eastern (MID) AF: 0.0109 AC: 3 AN: 274

European-Non Finnish (NFE) AF: 0.0175 AC: 1119 AN: 63796

Other (OTH) AF: 0.0124 AC: 22 AN: 1770

Alfa AF: 0.0185 Hom.: 738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs3998225; hg19: chr10-75709167;