rs6697016

Variant names:

• chr1-201438654-G-T
• rs6697016

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 0.278 in 151,950 control chromosomes in the GnomAD database, including 7,161 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 (7161 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467
• Publications: 6 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 = 0.471 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42214 AN: 151828 Hom.: 7161 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.278 AC: 42237 AN: 151950 Hom.: 7161 Cov.: 31 AF XY: 0.289 AC XY: 21472 AN XY: 74240

African (AFR) AF: 0.416 AC: 17233 AN: 41406

American (AMR) AF: 0.313 AC: 4771 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 642 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2509 AN: 5154

South Asian (SAS) AF: 0.452 AC: 2173 AN: 4808

European-Finnish (FIN) AF: 0.315 AC: 3324 AN: 10548

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10853 AN: 67986

Other (OTH) AF: 0.267 AC: 563 AN: 2112

Alfa AF: 0.202 Hom.: 16789

Bravo AF: 0.286

Asia WGS AF: 0.471 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs6697016; hg19: chr1-201407782;