1-109823461-T-C

Variant names:

• chr1-109823461-T-C
• rs484959

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 0.597 in 152,156 control chromosomes in the GnomAD database, including 29,900 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 0.60 (29900 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 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: 0.597 AC: 90796 AN: 152038 Hom.: 29850 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.597 AC: 90887 AN: 152156 Hom.: 29900 Cov.: 32 AF XY: 0.586 AC XY: 43612 AN XY: 74388

African (AFR) AF: 0.856 AC: 35546 AN: 41536

American (AMR) AF: 0.471 AC: 7196 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2205 AN: 3468

East Asian (EAS) AF: 0.145 AC: 751 AN: 5164

South Asian (SAS) AF: 0.536 AC: 2586 AN: 4824

European-Finnish (FIN) AF: 0.400 AC: 4235 AN: 10588

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36366 AN: 67968

Other (OTH) AF: 0.599 AC: 1267 AN: 2116

Alfa AF: 0.552 Hom.: 98410

Bravo AF: 0.609

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.2
DANN	Benign	0.75
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs484959; hg19: chr1-110366083;