rs61778086

Variant names:

• chr1-37860439-G-A
• rs61778086

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0306 AC: 1273 AN: 41576

American (AMR) AF: 0.101 AC: 1546 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 814 AN: 3472

East Asian (EAS) AF: 0.00366 AC: 19 AN: 5190

South Asian (SAS) AF: 0.135 AC: 654 AN: 4830

European-Finnish (FIN) AF: 0.0585 AC: 622 AN: 10626

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9143 AN: 68012

Other (OTH) AF: 0.139 AC: 292 AN: 2106

Alfa AF: 0.0994 Hom.: 127

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs61778086; hg19: chr1-38326111;