rs7903416

Variant names:

• chr10-33649088-T-C
• rs7903416

Your query was ambiguous. Multiple possible variants found:

• chr10-33649088-T-C
• chr10-33649088-T-G

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 0.341 in 152,162 control chromosomes in the GnomAD database, including 11,191 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 0.34 (11191 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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: 0.340 AC: 51741 AN: 152042 Hom.: 11164 Cov.: 33

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.341 AC: 51827 AN: 152162 Hom.: 11191 Cov.: 33 AF XY: 0.337 AC XY: 25063 AN XY: 74400

African (AFR) AF: 0.623 AC: 25867 AN: 41492

American (AMR) AF: 0.284 AC: 4339 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3468

East Asian (EAS) AF: 0.250 AC: 1292 AN: 5176

South Asian (SAS) AF: 0.273 AC: 1318 AN: 4824

European-Finnish (FIN) AF: 0.215 AC: 2274 AN: 10594

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14952 AN: 68006

Other (OTH) AF: 0.337 AC: 711 AN: 2112

Alfa AF: 0.124 Hom.: 181

Bravo AF: 0.366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.30
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs7903416; hg19: chr10-33938016;