1-22648435-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;