rs4970420

Variant names:

• chr1-1171093-G-A
• rs4970420

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 0.381 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
• Publications: 12 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 (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

African (AFR) AF: 0.705 AC: 29218 AN: 41466

American (AMR) AF: 0.337 AC: 5160 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 854 AN: 3466

East Asian (EAS) AF: 0.834 AC: 4286 AN: 5138

South Asian (SAS) AF: 0.420 AC: 2019 AN: 4812

European-Finnish (FIN) AF: 0.231 AC: 2444 AN: 10600

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13107 AN: 67974

Other (OTH) AF: 0.357 AC: 754 AN: 2110

Alfa AF: 0.245 Hom.: 3289

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
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs4970420; hg19: chr1-1106473;