rs6754295

Variant names:

• chr2-20983311-T-G
• rs6754295

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 0.276 in 152,012 control chromosomes in the GnomAD database, including 6,563 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 0.28 (6563 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

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 (EAS) allele frequency at 95% confidence interval = 0.692 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: 0.276 AC: 41946 AN: 151894 Hom.: 6562 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.276 AC: 41974 AN: 152012 Hom.: 6563 Cov.: 32 AF XY: 0.282 AC XY: 20939 AN XY: 74304

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.268

Alfa AF: 0.265 Hom.: 9781

Bravo AF: 0.272

Asia WGS AF: 0.588 AC: 2042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6754295; hg19: chr2-21206183;