rs681969

Variant names:

• chr1-35648632-C-T
• rs681969

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 0.935 in 152,292 control chromosomes in the GnomAD database, including 67,131 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 0.94 (67131 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 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: 0.935 AC: 142344 AN: 152174 Hom.: 67092 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.969

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.935 AC: 142438 AN: 152292 Hom.: 67131 Cov.: 33 AF XY: 0.937 AC XY: 69750 AN XY: 74472

African (AFR) AF: 0.802 AC: 33297 AN: 41528

American (AMR) AF: 0.969 AC: 14823 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3444 AN: 3470

East Asian (EAS) AF: 0.978 AC: 5074 AN: 5190

South Asian (SAS) AF: 0.928 AC: 4476 AN: 4824

European-Finnish (FIN) AF: 0.999 AC: 10616 AN: 10622

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67498 AN: 68042

Other (OTH) AF: 0.950 AC: 2010 AN: 2116

Alfa AF: 0.954 Hom.: 9005

Bravo AF: 0.929

Asia WGS AF: 0.947 AC: 3293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.60
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs681969; hg19: chr1-36114233;