rs4970420

Variant names:

• chr1-1171093-G-A
• rs4970420

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 0.381 in 152,062 control chromosomes in the GnomAD database, including 15,311 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 0.38 (15311 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782

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 (EAS) allele frequency at 95% confidence interval = 0.813 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: 0.381 AC: 57906 AN: 151940 Hom.: 15260 Cov.: 33

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.381 AC: 58011 AN: 152062 Hom.: 15311 Cov.: 33 AF XY: 0.386 AC XY: 28713 AN XY: 74338

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.357

Alfa AF: 0.249 Hom.: 3068

Bravo AF: 0.401

Asia WGS AF: 0.607 AC: 2109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4970420; hg19: chr1-1106473;