rs906071

Variant names:

• chr5-10109273-T-C
• rs906071

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 0.399 in 152,178 control chromosomes in the GnomAD database, including 14,434 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 0.40 (14434 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60586 AN: 152060 Hom.: 14385 Cov.: 33

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.399 AC: 60692 AN: 152178 Hom.: 14434 Cov.: 33 AF XY: 0.399 AC XY: 29707 AN XY: 74404

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.363

Alfa AF: 0.405 Hom.: 2071

Bravo AF: 0.405

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs906071; hg19: chr5-10109385;