1-186706395-A-G

Variant names:

• chr1-186706395-A-G
• rs6425043

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.023 in 152,268 control chromosomes in the GnomAD database, including 58 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 0.023 (58 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.023 (3507/152268) while in subpopulation NFE AF = 0.0359 (2443/68008). AF 95% confidence interval is 0.0347. There are 58 homozygotes in GnomAd4. There are 1700 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 58 gene

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: 0.0230 AC: 3505 AN: 152150 Hom.: 58 Cov.: 32

Gnomad AFR AF: 0.00596

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.00864

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0252

Gnomad FIN AF: 0.0388

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0359

Gnomad OTH AF: 0.0182

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

GnomAD4 genome AF: 0.0230 AC: 3507 AN: 152268 Hom.: 58 Cov.: 32 AF XY: 0.0228 AC XY: 1700 AN XY: 74456

African (AFR) AF: 0.00596 AC: 248 AN: 41576

American (AMR) AF: 0.0136 AC: 208 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00864 AC: 30 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0255 AC: 123 AN: 4828

European-Finnish (FIN) AF: 0.0388 AC: 411 AN: 10594

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0359 AC: 2443 AN: 68008

Other (OTH) AF: 0.0180 AC: 38 AN: 2112

Alfa AF: 0.0328 Hom.: 112

Bravo AF: 0.0204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.70
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs6425043; hg19: chr1-186675527;