chr10-106422755-A-G

Variant names:

• chr10-106422755-A-G
• rs2418804

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 0.642 in 151,842 control chromosomes in the GnomAD database, including 32,127 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 0.64 (32127 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 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: 0.642 AC: 97330 AN: 151722 Hom.: 32089 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.642 AC: 97426 AN: 151842 Hom.: 32127 Cov.: 32 AF XY: 0.639 AC XY: 47389 AN XY: 74178

African (AFR) AF: 0.782 AC: 32425 AN: 41470

American (AMR) AF: 0.570 AC: 8673 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2211 AN: 3464

East Asian (EAS) AF: 0.795 AC: 4095 AN: 5148

South Asian (SAS) AF: 0.665 AC: 3194 AN: 4806

European-Finnish (FIN) AF: 0.519 AC: 5477 AN: 10550

Middle Eastern (MID) AF: 0.753 AC: 220 AN: 292

European-Non Finnish (NFE) AF: 0.579 AC: 39319 AN: 67874

Other (OTH) AF: 0.651 AC: 1375 AN: 2112

Alfa AF: 0.609 Hom.: 15096

Bravo AF: 0.650

Asia WGS AF: 0.710 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.50
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs2418804; hg19: chr10-108182513;