rs10770974

chr12-23304638-T-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 0.361 in 152,090 control chromosomes in the GnomAD database, including 11,186 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 0.36 (11186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 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: 0.361 AC: 54882 AN: 151972 Hom.: 11198 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.361 AC: 54879 AN: 152090 Hom.: 11186 Cov.: 32 AF XY: 0.355 AC XY: 26372 AN XY: 74352

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.367

Alfa AF: 0.415 Hom.: 1715

Bravo AF: 0.348

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.5
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10770974; hg19: chr12-23457572;