10-70171890-C-A

Position:

• chr10-70171890-C-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 0.44 in 152,014 control chromosomes in the GnomAD database, including 15,374 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 0.44 (15374 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66765 AN: 151896 Hom.: 15342 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.381

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.440 AC: 66820 AN: 152014 Hom.: 15374 Cov.: 33 AF XY: 0.440 AC XY: 32688 AN XY: 74310

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.419

Alfa AF: 0.250 Hom.: 579

Bravo AF: 0.428

Asia WGS AF: 0.277 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.22
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2310991; hg19: chr10-71931646;