chr10-121449367-G-A

Position:

• chr10-121449367-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 0.436 in 151,816 control chromosomes in the GnomAD database, including 15,274 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 (15274 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.57 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: 0.436 AC: 66210 AN: 151698 Hom.: 15263 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.436 AC: 66234 AN: 151816 Hom.: 15274 Cov.: 31 AF XY: 0.438 AC XY: 32485 AN XY: 74166

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.452

Alfa AF: 0.487 Hom.: 37315

Bravo AF: 0.439

Asia WGS AF: 0.289 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2420936; hg19: chr10-123208881;