rs241215

Variant names:

• chr1-4544044-T-A
• rs241215

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 0.495 in 151,996 control chromosomes in the GnomAD database, including 20,162 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 0.49 (20162 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.826
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 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: 0.495 AC: 75177 AN: 151878 Hom.: 20159 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.495 AC: 75191 AN: 151996 Hom.: 20162 Cov.: 31 AF XY: 0.489 AC XY: 36308 AN XY: 74284

African (AFR) AF: 0.306 AC: 12703 AN: 41462

American (AMR) AF: 0.539 AC: 8235 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1691 AN: 3466

East Asian (EAS) AF: 0.295 AC: 1523 AN: 5160

South Asian (SAS) AF: 0.364 AC: 1750 AN: 4814

European-Finnish (FIN) AF: 0.596 AC: 6291 AN: 10552

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41217 AN: 67952

Other (OTH) AF: 0.513 AC: 1085 AN: 2114

Alfa AF: 0.555 Hom.: 3079

Bravo AF: 0.487

Asia WGS AF: 0.321 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.78
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs241215; hg19: chr1-4604104;