rs6425043

chr1-186706395-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 58 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00596

Gnomad4 AMR AF: 0.0136

Gnomad4 ASJ AF: 0.00864

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0255

Gnomad4 FIN AF: 0.0388

Gnomad4 NFE AF: 0.0359

Gnomad4 OTH AF: 0.0180

Alfa AF: 0.0290 Hom.: 10

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6425043; hg19: chr1-186675527;