rs3110127

Variant names:

• chr8-59217737-C-T
• rs3110127

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 0.423 in 151,842 control chromosomes in the GnomAD database, including 14,436 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 0.42 (14436 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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: 0.423 AC: 64138 AN: 151724 Hom.: 14401 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.423 AC: 64231 AN: 151842 Hom.: 14436 Cov.: 32 AF XY: 0.425 AC XY: 31544 AN XY: 74222

African (AFR) AF: 0.553 AC: 22896 AN: 41380

American (AMR) AF: 0.476 AC: 7269 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1354 AN: 3468

East Asian (EAS) AF: 0.614 AC: 3173 AN: 5170

South Asian (SAS) AF: 0.389 AC: 1874 AN: 4820

European-Finnish (FIN) AF: 0.367 AC: 3855 AN: 10508

Middle Eastern (MID) AF: 0.359 AC: 104 AN: 290

European-Non Finnish (NFE) AF: 0.331 AC: 22457 AN: 67934

Other (OTH) AF: 0.410 AC: 861 AN: 2098

Alfa AF: 0.366 Hom.: 42901

Bravo AF: 0.443

Asia WGS AF: 0.539 AC: 1879 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.30
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs3110127; hg19: chr8-60130296;