rs7210405

Positions:

• chr17-78650421-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.281

Alfa AF: 0.317 Hom.: 4437

Bravo AF: 0.280

Asia WGS AF: 0.347 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7210405; hg19: chr17-76646503;