rs4970518

Positions:

• chr1-27320591-T-C

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 0.229 in 152,110 control chromosomes in the GnomAD database, including 4,525 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 0.23 (4525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.34 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: 0.229 AC: 34769 AN: 151992 Hom.: 4526 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.229 AC: 34764 AN: 152110 Hom.: 4525 Cov.: 32 AF XY: 0.227 AC XY: 16903 AN XY: 74370

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.0666

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.248

Alfa AF: 0.281 Hom.: 8343

Bravo AF: 0.221

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4970518; hg19: chr1-27647082;