rs3754446

Variant names:

• chr1-109710619-A-C
• rs3754446

Your query was ambiguous. Multiple possible variants found:

• chr1-109710619-A-C
• chr1-109710619-A-G
• chr1-109710619-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 0.29 in 152,102 control chromosomes in the GnomAD database, including 8,216 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 0.29 (8216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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: 0.290 AC: 44104 AN: 151986 Hom.: 8211 Cov.: 32

Gnomad AFR AF: 0.0766

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.290 AC: 44109 AN: 152102 Hom.: 8216 Cov.: 32 AF XY: 0.295 AC XY: 21961 AN XY: 74350

African (AFR) AF: 0.0763 AC: 3169 AN: 41514

American (AMR) AF: 0.400 AC: 6110 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1286 AN: 3468

East Asian (EAS) AF: 0.695 AC: 3587 AN: 5158

South Asian (SAS) AF: 0.382 AC: 1836 AN: 4810

European-Finnish (FIN) AF: 0.370 AC: 3912 AN: 10580

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23297 AN: 67978

Other (OTH) AF: 0.323 AC: 683 AN: 2114

Alfa AF: 0.331 Hom.: 29401

Bravo AF: 0.285

Asia WGS AF: 0.492 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.3
DANN	Benign	0.57
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs3754446; hg19: chr1-110253241;