1-22648435-T-C

Variant names:

• chr1-22648435-T-C
• rs294179

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 0.578 in 152,058 control chromosomes in the GnomAD database, including 27,538 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 0.58 (27538 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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: 0.578 AC: 87820 AN: 151938 Hom.: 27490 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.578 AC: 87919 AN: 152058 Hom.: 27538 Cov.: 32 AF XY: 0.577 AC XY: 42917 AN XY: 74354

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.568

Alfa AF: 0.484 Hom.: 29645

Bravo AF: 0.597

Asia WGS AF: 0.662 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.7
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs294179; hg19: chr1-22974928;