chr5-127664245-G-A

Variant names:

• chr5-127664245-G-A
• rs248694
• ENST00000827053.1:n.195-477C>T

Variant summary

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

The ENST00000827053.1(ENSG00000248799):​n.195-477C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,046 control chromosomes in the GnomAD database, including 11,233 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 0.38 (11233 hom., cov: 32)
• Consequence: ENSG00000248799 ENST00000827053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 9 publications found

Genes affected

ENSG00000248799 (HGNC:59127):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827053.1. 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
	ENSG00000248799	ENST00000827053.1		n.195-477C>T		intron	N/A
	ENSG00000248799	ENST00000512352.1	TSL:5	n.-216C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57606 AN: 151928 Hom.: 11212 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.379 AC: 57658 AN: 152046 Hom.: 11233 Cov.: 32 AF XY: 0.371 AC XY: 27587 AN XY: 74340

African (AFR) AF: 0.384 AC: 15900 AN: 41452

American (AMR) AF: 0.326 AC: 4984 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1227 AN: 5178

South Asian (SAS) AF: 0.246 AC: 1182 AN: 4808

European-Finnish (FIN) AF: 0.361 AC: 3816 AN: 10578

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27897 AN: 67950

Other (OTH) AF: 0.383 AC: 807 AN: 2106

Alfa AF: 0.399 Hom.: 52501

Bravo AF: 0.377

Asia WGS AF: 0.227 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.27
PhyloP100		-0.28

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: rs248694;

hg19: chr5-126999937;