rs1438676

Variant names:

• chr5-110972184-T-C
• rs1438676
• ENST00000507627.1:n.483-1019A>G

Variant summary

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

The ENST00000757131.1(ENSG00000298655):​n.115-734T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,104 control chromosomes in the GnomAD database, including 8,118 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 0.25 (8118 hom., cov: 33)
• Consequence: ENSG00000298655 ENST00000757131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 2 publications found

Genes affected

ENSG00000248428 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757131.1. 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
	ENSG00000248428	ENST00000507627.1	TSL:5	n.483-1019A>G		intron	N/A
	ENSG00000298655	ENST00000757131.1		n.115-734T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37274 AN: 151986 Hom.: 8083 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.0886

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0831

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.246 AC: 37377 AN: 152104 Hom.: 8118 Cov.: 33 AF XY: 0.245 AC XY: 18184 AN XY: 74368

African (AFR) AF: 0.580 AC: 24072 AN: 41482

American (AMR) AF: 0.212 AC: 3244 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0886 AC: 307 AN: 3466

East Asian (EAS) AF: 0.276 AC: 1426 AN: 5174

South Asian (SAS) AF: 0.198 AC: 955 AN: 4822

European-Finnish (FIN) AF: 0.105 AC: 1115 AN: 10618

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0831 AC: 5646 AN: 67942

Other (OTH) AF: 0.225 AC: 476 AN: 2116

Alfa AF: 0.125 Hom.: 1219

Bravo AF: 0.267

Asia WGS AF: 0.242 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.84
PhyloP100		-0.23

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: rs1438676;

hg19: chr5-110307883;