rs6757804

Variant names:

• chr2-150779318-C-T
• rs6757804

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 0.58 in 151,812 control chromosomes in the GnomAD database, including 25,855 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 0.58 (25855 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88072 AN: 151694 Hom.: 25839 Cov.: 30

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.580 AC: 88124 AN: 151812 Hom.: 25855 Cov.: 30 AF XY: 0.575 AC XY: 42656 AN XY: 74154

African (AFR) AF: 0.558 AC: 23082 AN: 41382

American (AMR) AF: 0.664 AC: 10142 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1831 AN: 3466

East Asian (EAS) AF: 0.592 AC: 3056 AN: 5166

South Asian (SAS) AF: 0.588 AC: 2824 AN: 4804

European-Finnish (FIN) AF: 0.451 AC: 4730 AN: 10498

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40431 AN: 67922

Other (OTH) AF: 0.578 AC: 1215 AN: 2102

Alfa AF: 0.591 Hom.: 76165

Bravo AF: 0.596

Asia WGS AF: 0.598 AC: 2083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.035
DANN	Benign	0.13
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6757804; hg19: chr2-151635832;