chr1-205754444-C-T

Variant names:

• chr1-205754444-C-T
• rs823118

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 0.457 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
• Publications: 80 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.235 AC: 9757 AN: 41472

American (AMR) AF: 0.439 AC: 6690 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2024 AN: 3466

East Asian (EAS) AF: 0.542 AC: 2803 AN: 5168

South Asian (SAS) AF: 0.526 AC: 2513 AN: 4780

European-Finnish (FIN) AF: 0.594 AC: 6260 AN: 10532

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37652 AN: 67940

Other (OTH) AF: 0.492 AC: 1038 AN: 2110

Alfa AF: 0.518 Hom.: 40472

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
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs823118; hg19: chr1-205723572;