rs6688464

Variant names:

• chr1-35706594-G-A
• rs6688464

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 0.664 in 152,106 control chromosomes in the GnomAD database, including 38,243 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 0.66 (38243 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.864 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: 0.664 AC: 100966 AN: 151988 Hom.: 38250 Cov.: 33

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.664 AC: 100969 AN: 152106 Hom.: 38243 Cov.: 33 AF XY: 0.659 AC XY: 49011 AN XY: 74360

African (AFR) AF: 0.327 AC: 13562 AN: 41428

American (AMR) AF: 0.618 AC: 9445 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2697 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1150 AN: 5174

South Asian (SAS) AF: 0.765 AC: 3690 AN: 4824

European-Finnish (FIN) AF: 0.829 AC: 8783 AN: 10590

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59174 AN: 68024

Other (OTH) AF: 0.688 AC: 1453 AN: 2112

Alfa AF: 0.771 Hom.: 11264

Bravo AF: 0.626

Asia WGS AF: 0.505 AC: 1761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.9
DANN	Benign	0.77
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs6688464; hg19: chr1-36172195;