rs4907110

Positions:

• chr1-84905582-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;