rs4673301

Variant names:

• chr2-204503735-T-C
• rs4673301
• ENST00000456384.1:n.269-3880T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456384.1(ENSG00000237843):​n.269-3880T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 152,212 control chromosomes in the GnomAD database, including 377 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 0.054 (377 hom., cov: 33)
• Consequence: ENSG00000237843 ENST00000456384.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224

Genes affected

ENSG00000237843 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 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
ENSG00000237843	ENST00000456384.1	n.269-3880T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0541 AC: 8229 AN: 152092 Hom.: 374 Cov.: 33

Gnomad AFR AF: 0.0621

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0306

Gnomad ASJ AF: 0.0485

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.0344

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0542 AC: 8248 AN: 152212 Hom.: 377 Cov.: 33 AF XY: 0.0552 AC XY: 4108 AN XY: 74416

Gnomad4 AFR AF: 0.0622

Gnomad4 AMR AF: 0.0308

Gnomad4 ASJ AF: 0.0485

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.0980

Gnomad4 FIN AF: 0.0344

Gnomad4 NFE AF: 0.0384

Gnomad4 OTH AF: 0.0545

Alfa AF: 0.0423 Hom.: 254

Bravo AF: 0.0539

Asia WGS AF: 0.219 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4673301; hg19: chr2-205368458;