1-1237527-C-T

Position:

• chr1-1237527-C-T

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 0.037 in 152,332 control chromosomes in the GnomAD database, including 161 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 0.037 (161 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0564 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: 0.0371 AC: 5644 AN: 152214 Hom.: 161 Cov.: 34

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.0593

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0192

Gnomad FIN AF: 0.0143

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0370 AC: 5643 AN: 152332 Hom.: 161 Cov.: 34 AF XY: 0.0350 AC XY: 2610 AN XY: 74492

Gnomad4 AFR AF: 0.0104

Gnomad4 AMR AF: 0.0390

Gnomad4 ASJ AF: 0.0593

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0190

Gnomad4 FIN AF: 0.0143

Gnomad4 NFE AF: 0.0579

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0437 Hom.: 92

Bravo AF: 0.0385

Asia WGS AF: 0.00982 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs715643; hg19: chr1-1172907;