rs4907110

Variant names:

• chr1-84905582-C-T
• rs4907110

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 0.397 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.397 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

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.377

Alfa AF: 0.352 Hom.: 19782

Bravo AF: 0.390

Asia WGS AF: 0.414 AC: 1435 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4907110; hg19: chr1-85371265;