rs3110127

Variant names:

• chr8-59217737-C-T
• rs3110127

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.423 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

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.410

Alfa AF: 0.356 Hom.: 21506

Bravo AF: 0.443

Asia WGS AF: 0.539 AC: 1879 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3110127; hg19: chr8-60130296;