rs1876525

Variant names:

• chr6-86442374-C-G
• rs1876525

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 0.0702 in 152,214 control chromosomes in the GnomAD database, including 493 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 0.070 (493 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 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: 0.0702 AC: 10682 AN: 152096 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.0261

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0349

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0702 AC: 10686 AN: 152214 Hom.: 493 Cov.: 32 AF XY: 0.0710 AC XY: 5281 AN XY: 74422

African (AFR) AF: 0.0263 AC: 1094 AN: 41546

American (AMR) AF: 0.0816 AC: 1247 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3466

East Asian (EAS) AF: 0.0349 AC: 181 AN: 5180

South Asian (SAS) AF: 0.137 AC: 660 AN: 4824

European-Finnish (FIN) AF: 0.0744 AC: 789 AN: 10598

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0866 AC: 5891 AN: 68006

Other (OTH) AF: 0.0909 AC: 192 AN: 2112

Alfa AF: 0.0705 Hom.: 52

Bravo AF: 0.0665

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.83
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs1876525; hg19: chr6-87152092;