rs7210405

Variant names:

• chr17-78650421-G-A
• rs7210405

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 0.296 in 152,026 control chromosomes in the GnomAD database, including 7,104 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 0.30 (7104 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

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: 0.296 AC: 44941 AN: 151908 Hom.: 7106 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.296 AC: 44948 AN: 152026 Hom.: 7104 Cov.: 33 AF XY: 0.300 AC XY: 22299 AN XY: 74288

African (AFR) AF: 0.198 AC: 8204 AN: 41468

American (AMR) AF: 0.279 AC: 4264 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 752 AN: 3472

East Asian (EAS) AF: 0.398 AC: 2056 AN: 5164

South Asian (SAS) AF: 0.284 AC: 1370 AN: 4816

European-Finnish (FIN) AF: 0.406 AC: 4275 AN: 10532

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23013 AN: 67964

Other (OTH) AF: 0.281 AC: 594 AN: 2116

Alfa AF: 0.316 Hom.: 5940

Bravo AF: 0.280

Asia WGS AF: 0.347 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.81
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs7210405; hg19: chr17-76646503;