1-220440171-T-C

Variant names:

• chr1-220440171-T-C
• rs1338775

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 0.877 in 152,240 control chromosomes in the GnomAD database, including 59,999 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 0.88 (59999 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.962 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: 0.877 AC: 133436 AN: 152122 Hom.: 59983 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.877 AC: 133511 AN: 152240 Hom.: 59999 Cov.: 32 AF XY: 0.881 AC XY: 65554 AN XY: 74420

African (AFR) AF: 0.655 AC: 27192 AN: 41506

American (AMR) AF: 0.948 AC: 14507 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3310 AN: 3472

East Asian (EAS) AF: 0.916 AC: 4742 AN: 5178

South Asian (SAS) AF: 0.950 AC: 4581 AN: 4824

European-Finnish (FIN) AF: 0.966 AC: 10259 AN: 10616

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.968 AC: 65883 AN: 68028

Other (OTH) AF: 0.912 AC: 1929 AN: 2114

Alfa AF: 0.948 Hom.: 113288

Bravo AF: 0.866

Asia WGS AF: 0.911 AC: 3168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.33
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs1338775; hg19: chr1-220613513;