rs7557548

Variant names:

• chr2-57438494-A-G
• rs7557548
• ENST00000811252.1:n.147-58364T>C

Variant summary

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

The ENST00000811252.1(ENSG00000285755):​n.147-58364T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,500 control chromosomes in the GnomAD database, including 6,353 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 0.27 (6353 hom., cov: 31)
• Consequence: ENSG00000285755 ENST00000811252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 1 publications found

Genes affected

ENSG00000285755 (HGNC:58935):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811252.1. 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
	ENSG00000285755	ENST00000811252.1		n.147-58364T>C		intron	N/A
	ENSG00000285755	ENST00000811254.1		n.54+2637T>C		intron	N/A
	ENSG00000285755	ENST00000811260.1		n.54+2637T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40447 AN: 151382 Hom.: 6329 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.267 AC: 40510 AN: 151500 Hom.: 6353 Cov.: 31 AF XY: 0.265 AC XY: 19608 AN XY: 74004

African (AFR) AF: 0.437 AC: 18066 AN: 41304

American (AMR) AF: 0.178 AC: 2707 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3464

East Asian (EAS) AF: 0.0576 AC: 298 AN: 5176

South Asian (SAS) AF: 0.279 AC: 1340 AN: 4802

European-Finnish (FIN) AF: 0.205 AC: 2151 AN: 10512

Middle Eastern (MID) AF: 0.341 AC: 99 AN: 290

European-Non Finnish (NFE) AF: 0.211 AC: 14318 AN: 67730

Other (OTH) AF: 0.240 AC: 506 AN: 2112

Alfa AF: 0.249 Hom.: 2122

Bravo AF: 0.267

Asia WGS AF: 0.198 AC: 688 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.75
PhyloP100		1.3

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: rs7557548;

hg19: chr2-57665629;