1-205754444-C-T

Variant names:

• chr1-205754444-C-T
• rs823118

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 0.457 in 151,926 control chromosomes in the GnomAD database, including 17,544 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 0.46 (17544 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 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: 0.457 AC: 69396 AN: 151808 Hom.: 17540 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.457 AC: 69409 AN: 151926 Hom.: 17544 Cov.: 31 AF XY: 0.459 AC XY: 34080 AN XY: 74256

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.492

Alfa AF: 0.541 Hom.: 8749

Bravo AF: 0.432

Asia WGS AF: 0.517 AC: 1799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.70
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs823118; hg19: chr1-205723572;