rs4865673

Variant names:

• chr5-51632976-G-A
• rs4865673
• ENST00000666280.1:n.435+31638C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000666280.1(ENSG00000288035):​n.435+31638C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,978 control chromosomes in the GnomAD database, including 6,636 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 0.29 (6636 hom., cov: 32)
• Consequence: ENSG00000288035 ENST00000666280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 8 publications found

Genes affected

ENSG00000288035 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666280.1. 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
	ENSG00000288035	ENST00000666280.1		n.435+31638C>T		intron	N/A
	ENSG00000288035	ENST00000730931.1		n.110+31638C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43976 AN: 151858 Hom.: 6631 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.0703

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.289 AC: 43997 AN: 151978 Hom.: 6636 Cov.: 32 AF XY: 0.285 AC XY: 21192 AN XY: 74270

African (AFR) AF: 0.267 AC: 11053 AN: 41430

American (AMR) AF: 0.304 AC: 4649 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1087 AN: 3472

East Asian (EAS) AF: 0.0707 AC: 364 AN: 5148

South Asian (SAS) AF: 0.220 AC: 1059 AN: 4822

European-Finnish (FIN) AF: 0.268 AC: 2832 AN: 10558

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21800 AN: 67954

Other (OTH) AF: 0.286 AC: 605 AN: 2112

Alfa AF: 0.312 Hom.: 32388

Bravo AF: 0.289

Asia WGS AF: 0.173 AC: 602 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.6
DANN	Benign	0.46
PhyloP100		0.023

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4865673;

hg19: chr5-50928810;