rs10770974

Variant names:

• chr12-23304638-T-A
• rs10770974

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 0.361 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.198 AC: 8225 AN: 41506

American (AMR) AF: 0.380 AC: 5803 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3468

East Asian (EAS) AF: 0.111 AC: 571 AN: 5164

South Asian (SAS) AF: 0.334 AC: 1609 AN: 4820

European-Finnish (FIN) AF: 0.364 AC: 3848 AN: 10570

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32615 AN: 67962

Other (OTH) AF: 0.367 AC: 775 AN: 2110

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
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs10770974; hg19: chr12-23457572;