chr1-37860439-G-A

Variant names:

• chr1-37860439-G-A
• rs61778086

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;