rs4907110

Variant names:

• chr1-84905582-C-T
• rs4907110

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 0.397 in 151,914 control chromosomes in the GnomAD database, including 12,502 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 0.40 (12502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 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: 0.397 AC: 60281 AN: 151796 Hom.: 12475 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.397 AC: 60355 AN: 151914 Hom.: 12502 Cov.: 32 AF XY: 0.398 AC XY: 29560 AN XY: 74234

African (AFR) AF: 0.502 AC: 20804 AN: 41416

American (AMR) AF: 0.291 AC: 4443 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3472

East Asian (EAS) AF: 0.454 AC: 2331 AN: 5132

South Asian (SAS) AF: 0.406 AC: 1959 AN: 4822

European-Finnish (FIN) AF: 0.426 AC: 4487 AN: 10528

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23940 AN: 67962

Other (OTH) AF: 0.377 AC: 794 AN: 2108

Alfa AF: 0.361 Hom.: 43129

Bravo AF: 0.390

Asia WGS AF: 0.414 AC: 1435 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.76
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs4907110; hg19: chr1-85371265;