rs4673301

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000237843 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456384.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000237843	ENST00000456384.1	TSL:3	n.269-3880T>C		intron	N/A

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

African (AFR) AF: 0.0622 AC: 2584 AN: 41538

American (AMR) AF: 0.0308 AC: 471 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0485 AC: 168 AN: 3466

East Asian (EAS) AF: 0.276 AC: 1426 AN: 5166

South Asian (SAS) AF: 0.0980 AC: 472 AN: 4814

European-Finnish (FIN) AF: 0.0344 AC: 365 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0384 AC: 2614 AN: 68016

Other (OTH) AF: 0.0545 AC: 115 AN: 2112

Alfa AF: 0.0465 Hom.: 524

Bravo AF: 0.0539

Asia WGS AF: 0.219 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.76
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4673301; hg19: chr2-205368458;