rs2180619

Variant names:

• chr6-88168233-G-A
• rs2180619

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 0.532 in 151,944 control chromosomes in the GnomAD database, including 22,341 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 0.53 (22341 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 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: 0.532 AC: 80810 AN: 151826 Hom.: 22338 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.622

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.532 AC: 80849 AN: 151944 Hom.: 22341 Cov.: 31 AF XY: 0.534 AC XY: 39643 AN XY: 74250

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.562

Alfa AF: 0.585 Hom.: 34256

Bravo AF: 0.526

Asia WGS AF: 0.628 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.34
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2180619; hg19: chr6-88877952;