rs2338

Variant names:

• chr6-1573378-G-A
• rs2338

Your query was ambiguous. Multiple possible variants found:

• chr6-1573378-G-A
• chr6-1573378-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 0.289 in 152,134 control chromosomes in the GnomAD database, including 6,709 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 0.29 (6709 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 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: 0.289 AC: 43938 AN: 152020 Hom.: 6701 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.289 AC: 43975 AN: 152134 Hom.: 6709 Cov.: 33 AF XY: 0.294 AC XY: 21894 AN XY: 74386

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.341

Alfa AF: 0.285 Hom.: 11917

Bravo AF: 0.299

Asia WGS AF: 0.329 AC: 1140 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2338; hg19: chr6-1573613;