rs4471299

Variant names:

• chr1-200484291-T-C
• rs4471299

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 0.595 in 151,812 control chromosomes in the GnomAD database, including 27,472 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 0.59 (27472 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 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: 0.595 AC: 90196 AN: 151694 Hom.: 27448 Cov.: 30

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.595 AC: 90263 AN: 151812 Hom.: 27472 Cov.: 30 AF XY: 0.588 AC XY: 43650 AN XY: 74190

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.600

Alfa AF: 0.578 Hom.: 3206

Bravo AF: 0.612

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.015
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4471299; hg19: chr1-200453419;