1-220440171-T-C

Variant names:

• chr1-220440171-T-C
• rs1338775

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.948

Gnomad4 ASJ AF: 0.953

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.950

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.968

Gnomad4 OTH AF: 0.912

Alfa AF: 0.956 Hom.: 92348

Bravo AF: 0.866

Asia WGS AF: 0.911 AC: 3168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1338775; hg19: chr1-220613513;