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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.186 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

Gnomad4 AFR AF: 0.0442

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.183

Alfa AF: 0.243 Hom.: 6891

Bravo AF: 0.169

Asia WGS AF: 0.122 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2250264; hg19: chr6-30821187;