1-40609537-C-T

Variant names:

• chr1-40609537-C-T
• rs500586

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 0.68 in 151,992 control chromosomes in the GnomAD database, including 35,457 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 0.68 (35457 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 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: 0.680 AC: 103293 AN: 151874 Hom.: 35450 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.680 AC: 103349 AN: 151992 Hom.: 35457 Cov.: 31 AF XY: 0.674 AC XY: 50081 AN XY: 74270

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.673

Alfa AF: 0.677 Hom.: 45308

Bravo AF: 0.681

Asia WGS AF: 0.541 AC: 1881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs500586; hg19: chr1-41075209;