rs2250264

Variant names:

• chr6-30853410-G-A
• rs2250264

Your query was ambiguous. Multiple possible variants found:

• chr6-30853410-G-A
• chr6-30853410-G-C

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 0.185 in 152,030 control chromosomes in the GnomAD database, including 3,319 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 0.19 (3319 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28196 AN: 151912 Hom.: 3319 Cov.: 31

Gnomad AFR AF: 0.0444

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.185 AC: 28191 AN: 152030 Hom.: 3319 Cov.: 31 AF XY: 0.187 AC XY: 13907 AN XY: 74294

African (AFR) AF: 0.0442 AC: 1835 AN: 41490

American (AMR) AF: 0.171 AC: 2606 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 954 AN: 3470

East Asian (EAS) AF: 0.129 AC: 669 AN: 5168

South Asian (SAS) AF: 0.178 AC: 857 AN: 4828

European-Finnish (FIN) AF: 0.311 AC: 3279 AN: 10534

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17288 AN: 67966

Other (OTH) AF: 0.183 AC: 386 AN: 2104

Alfa AF: 0.229 Hom.: 16466

Bravo AF: 0.169

Asia WGS AF: 0.122 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.7
DANN	Benign	0.94
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2250264; hg19: chr6-30821187;