rs6754295

Variant names:

• chr2-20983311-T-G
• rs6754295

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 0.276 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
• Publications: 45 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.271 AC: 11234 AN: 41446

American (AMR) AF: 0.240 AC: 3670 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 953 AN: 3466

East Asian (EAS) AF: 0.712 AC: 3652 AN: 5132

South Asian (SAS) AF: 0.534 AC: 2569 AN: 4810

European-Finnish (FIN) AF: 0.273 AC: 2884 AN: 10580

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16135 AN: 67978

Other (OTH) AF: 0.268 AC: 565 AN: 2108

Alfa AF: 0.262 Hom.: 21777

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
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs6754295; hg19: chr2-21206183;