chr1-24967773-G-A

Position:

• chr1-24967773-G-A

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 0.471 in 152,022 control chromosomes in the GnomAD database, including 18,317 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 0.47 (18317 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.707

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71622 AN: 151904 Hom.: 18288 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.471 AC: 71670 AN: 152022 Hom.: 18317 Cov.: 32 AF XY: 0.487 AC XY: 36165 AN XY: 74300

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.510

Alfa AF: 0.499 Hom.: 14369

Bravo AF: 0.468

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7523412; hg19: chr1-25294264;