rs4970518

Variant names:

• chr1-27320591-T-C
• rs4970518

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 0.229 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.130 AC: 5379 AN: 41508

American (AMR) AF: 0.224 AC: 3416 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1108 AN: 3470

East Asian (EAS) AF: 0.0666 AC: 345 AN: 5184

South Asian (SAS) AF: 0.354 AC: 1707 AN: 4818

European-Finnish (FIN) AF: 0.235 AC: 2485 AN: 10588

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19446 AN: 67958

Other (OTH) AF: 0.248 AC: 522 AN: 2108

Alfa AF: 0.272 Hom.: 10935

Bravo AF: 0.221

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.70
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs4970518; hg19: chr1-27647082;