chr1-37860439-G-A

Position:

• chr1-37860439-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 0.0956 in 152,316 control chromosomes in the GnomAD database, including 872 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 0.096 (872 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 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: 0.0957 AC: 14570 AN: 152198 Hom.: 872 Cov.: 33

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.00365

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.0956 AC: 14563 AN: 152316 Hom.: 872 Cov.: 33 AF XY: 0.0918 AC XY: 6838 AN XY: 74484

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.00366

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0585

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.139

Alfa AF: 0.102 Hom.: 125

Bravo AF: 0.0945

Asia WGS AF: 0.0550 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	15
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61778086; hg19: chr1-38326111;