rs527248

Variant names:

• chr1-177906379-A-G
• rs527248
• ENST00000664407.1:n.71+13703T>C

Variant summary

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

The ENST00000664407.1(ENSG00000227579):​n.71+13703T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,206 control chromosomes in the GnomAD database, including 2,229 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 0.16 (2229 hom., cov: 32)
• Consequence: ENSG00000227579 ENST00000664407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654
• Publications: 17 publications found

Genes affected

ENSG00000227579 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664407.1. 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
	ENSG00000227579	ENST00000664407.1		n.71+13703T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24990 AN: 152088 Hom.: 2230 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.164 AC: 24997 AN: 152206 Hom.: 2229 Cov.: 32 AF XY: 0.164 AC XY: 12232 AN XY: 74422

African (AFR) AF: 0.104 AC: 4339 AN: 41544

American (AMR) AF: 0.195 AC: 2979 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3466

East Asian (EAS) AF: 0.171 AC: 883 AN: 5172

South Asian (SAS) AF: 0.146 AC: 706 AN: 4820

European-Finnish (FIN) AF: 0.173 AC: 1832 AN: 10604

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13297 AN: 67992

Other (OTH) AF: 0.160 AC: 338 AN: 2114

Alfa AF: 0.171 Hom.: 427

Bravo AF: 0.164

Asia WGS AF: 0.137 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		0.65

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: rs527248;

hg19: chr1-177875514;