chr1-248330209-T-C

Variant names:

• chr1-248330209-T-C
• rs4244187

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 0.787 in 151,952 control chromosomes in the GnomAD database, including 47,464 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 0.79 (47464 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.852 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: 0.787 AC: 119553 AN: 151832 Hom.: 47423 Cov.: 31

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.787 AC: 119650 AN: 151952 Hom.: 47464 Cov.: 31 AF XY: 0.792 AC XY: 58807 AN XY: 74252

African (AFR) AF: 0.853 AC: 35407 AN: 41486

American (AMR) AF: 0.784 AC: 11970 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2430 AN: 3468

East Asian (EAS) AF: 0.859 AC: 4451 AN: 5180

South Asian (SAS) AF: 0.874 AC: 4205 AN: 4812

European-Finnish (FIN) AF: 0.802 AC: 8409 AN: 10484

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50169 AN: 67942

Other (OTH) AF: 0.766 AC: 1615 AN: 2108

Alfa AF: 0.748 Hom.: 174434

Bravo AF: 0.787

Asia WGS AF: 0.859 AC: 2982 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.31
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4244187; hg19: chr1-248493511;