1-217419603-A-G

Variant names:

• chr1-217419603-A-G
• rs265120

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 0.176 in 152,184 control chromosomes in the GnomAD database, including 3,510 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 0.18 (3510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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: 0.176 AC: 26704 AN: 152066 Hom.: 3493 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.0630

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.176 AC: 26759 AN: 152184 Hom.: 3510 Cov.: 32 AF XY: 0.170 AC XY: 12662 AN XY: 74402

African (AFR) AF: 0.367 AC: 15233 AN: 41476

American (AMR) AF: 0.120 AC: 1836 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5186

South Asian (SAS) AF: 0.0782 AC: 377 AN: 4818

European-Finnish (FIN) AF: 0.0630 AC: 669 AN: 10614

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7505 AN: 68006

Other (OTH) AF: 0.160 AC: 338 AN: 2112

Alfa AF: 0.127 Hom.: 707

Bravo AF: 0.190

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.9
DANN	Benign	0.74
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs265120; hg19: chr1-217592945;