chr1-2414660-C-G

Variant names:

• chr1-2414660-C-G
• rs7556447

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 0.199 in 152,212 control chromosomes in the GnomAD database, including 3,505 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 0.20 (3505 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30353 AN: 152094 Hom.: 3505 Cov.: 33

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.199 AC: 30352 AN: 152212 Hom.: 3505 Cov.: 33 AF XY: 0.201 AC XY: 14974 AN XY: 74420

African (AFR) AF: 0.0983 AC: 4085 AN: 41546

American (AMR) AF: 0.147 AC: 2248 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3472

East Asian (EAS) AF: 0.168 AC: 868 AN: 5168

South Asian (SAS) AF: 0.175 AC: 844 AN: 4828

European-Finnish (FIN) AF: 0.332 AC: 3513 AN: 10580

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17300 AN: 67996

Other (OTH) AF: 0.211 AC: 447 AN: 2114

Alfa AF: 0.230 Hom.: 535

Bravo AF: 0.183

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.40
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs7556447; hg19: chr1-2346099;