rs6702767

Variant names:

• chr1-200875419-A-G
• rs6702767

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 0.411 in 152,070 control chromosomes in the GnomAD database, including 14,064 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 0.41 (14064 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 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: 0.412 AC: 62531 AN: 151952 Hom.: 14057 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.411 AC: 62571 AN: 152070 Hom.: 14064 Cov.: 32 AF XY: 0.405 AC XY: 30096 AN XY: 74322

African (AFR) AF: 0.253 AC: 10509 AN: 41468

American (AMR) AF: 0.424 AC: 6488 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1488 AN: 3472

East Asian (EAS) AF: 0.304 AC: 1571 AN: 5164

South Asian (SAS) AF: 0.337 AC: 1625 AN: 4816

European-Finnish (FIN) AF: 0.393 AC: 4150 AN: 10566

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35041 AN: 67972

Other (OTH) AF: 0.454 AC: 959 AN: 2112

Alfa AF: 0.434 Hom.: 1920

Bravo AF: 0.410

Asia WGS AF: 0.327 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.51
DANN	Benign	0.40
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs6702767; hg19: chr1-200844547;