rs669408

Variant names:

• chr1-232383404-A-C
• rs669408

Your query was ambiguous. Multiple possible variants found:

• chr1-232383404-A-C
• chr1-232383404-A-G
• chr1-232383404-A-T

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 0.514 in 151,928 control chromosomes in the GnomAD database, including 21,649 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 0.51 (21649 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 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: 0.513 AC: 77951 AN: 151810 Hom.: 21614 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.514 AC: 78034 AN: 151928 Hom.: 21649 Cov.: 32 AF XY: 0.517 AC XY: 38352 AN XY: 74248

African (AFR) AF: 0.712 AC: 29480 AN: 41418

American (AMR) AF: 0.495 AC: 7556 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1327 AN: 3472

East Asian (EAS) AF: 0.727 AC: 3750 AN: 5156

South Asian (SAS) AF: 0.416 AC: 1999 AN: 4810

European-Finnish (FIN) AF: 0.496 AC: 5234 AN: 10554

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27469 AN: 67950

Other (OTH) AF: 0.469 AC: 990 AN: 2112

Alfa AF: 0.440 Hom.: 18798

Bravo AF: 0.525

Asia WGS AF: 0.570 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.25
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs669408; hg19: chr1-232519150;