1-217264584-A-G

Variant names:

• chr1-217264584-A-G
• rs10495052

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 0.0321 in 152,168 control chromosomes in the GnomAD database, including 105 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 0.032 (105 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0689 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: 0.0321 AC: 4881 AN: 152050 Hom.: 105 Cov.: 31

Gnomad AFR AF: 0.0429

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0288

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0321 AC: 4886 AN: 152168 Hom.: 105 Cov.: 31 AF XY: 0.0327 AC XY: 2437 AN XY: 74414

African (AFR) AF: 0.0429 AC: 1779 AN: 41498

American (AMR) AF: 0.0227 AC: 347 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 136 AN: 3470

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5176

South Asian (SAS) AF: 0.0753 AC: 363 AN: 4822

European-Finnish (FIN) AF: 0.0155 AC: 164 AN: 10602

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0288 AC: 1956 AN: 68006

Other (OTH) AF: 0.0336 AC: 71 AN: 2112

Alfa AF: 0.0335 Hom.: 8

Bravo AF: 0.0325

Asia WGS AF: 0.0210 AC: 74 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	1.2
DANN	Benign	0.72
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs10495052; hg19: chr1-217437926;