chr10-4434217-A-G

Variant names:

• chr10-4434217-A-G
• rs1751277

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 0.328 in 152,054 control chromosomes in the GnomAD database, including 10,148 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 0.33 (10148 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49818 AN: 151936 Hom.: 10121 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.328 AC: 49903 AN: 152054 Hom.: 10148 Cov.: 32 AF XY: 0.334 AC XY: 24798 AN XY: 74348

African (AFR) AF: 0.501 AC: 20740 AN: 41430

American (AMR) AF: 0.318 AC: 4865 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3470

East Asian (EAS) AF: 0.767 AC: 3951 AN: 5150

South Asian (SAS) AF: 0.510 AC: 2458 AN: 4824

European-Finnish (FIN) AF: 0.165 AC: 1750 AN: 10598

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14306 AN: 67970

Other (OTH) AF: 0.311 AC: 657 AN: 2110

Alfa AF: 0.249 Hom.: 3341

Bravo AF: 0.342

Asia WGS AF: 0.610 AC: 2122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.34
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1751277; hg19: chr10-4476409;