rs6754295

Positions:

• chr2-20983311-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 0.276 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;