rs1000623

chr2-186920337-T-G

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 0.0591 in 152,288 control chromosomes in the GnomAD database, including 382 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 0.059 (382 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0841 is higher than 0.05.

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: 0.0591 AC: 8996 AN: 152170 Hom.: 382 Cov.: 33

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0493

Gnomad ASJ AF: 0.0593

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00889

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0859

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0591 AC: 8994 AN: 152288 Hom.: 382 Cov.: 33 AF XY: 0.0589 AC XY: 4386 AN XY: 74466

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.0492

Gnomad4 ASJ AF: 0.0593

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00890

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0859

Gnomad4 OTH AF: 0.0535

Alfa AF: 0.0833 Hom.: 88

Bravo AF: 0.0512

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.1
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: rs1000623; hg19: chr2-187785064;