chr1-24150396-A-G

Variant names:

• chr1-24150396-A-G
• rs11579657

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 0.155 in 152,148 control chromosomes in the GnomAD database, including 2,303 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 0.16 (2303 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 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: 0.156 AC: 23651 AN: 152030 Hom.: 2301 Cov.: 33

Gnomad AFR AF: 0.0520

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.0937

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.155 AC: 23647 AN: 152148 Hom.: 2303 Cov.: 33 AF XY: 0.155 AC XY: 11510 AN XY: 74386

Gnomad4 AFR AF: 0.0518

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0772

Gnomad4 SAS AF: 0.0933

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.175

Alfa AF: 0.191 Hom.: 3844

Bravo AF: 0.157

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11579657; hg19: chr1-24476886;