1-101284418-A-G

Variant names:

• chr1-101284418-A-G
• rs910633

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 0.506 in 152,058 control chromosomes in the GnomAD database, including 19,761 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 0.51 (19761 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76838 AN: 151940 Hom.: 19736 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.506 AC: 76893 AN: 152058 Hom.: 19761 Cov.: 33 AF XY: 0.500 AC XY: 37178 AN XY: 74348

African (AFR) AF: 0.580 AC: 24037 AN: 41460

American (AMR) AF: 0.425 AC: 6499 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1735 AN: 3472

East Asian (EAS) AF: 0.373 AC: 1930 AN: 5178

South Asian (SAS) AF: 0.568 AC: 2744 AN: 4828

European-Finnish (FIN) AF: 0.409 AC: 4321 AN: 10574

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33943 AN: 67948

Other (OTH) AF: 0.507 AC: 1070 AN: 2112

Alfa AF: 0.502 Hom.: 58027

Bravo AF: 0.505

Asia WGS AF: 0.529 AC: 1840 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	7.8
DANN	Benign	0.38
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs910633; hg19: chr1-101749974;