rs1554472

Variant names:

• chr4-156568754-G-A
• rs1554472
• ENST00000720474.1:n.103+657G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-156568754-G-A
• chr4-156568754-G-C
• chr4-156568754-G-T

Variant summary

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

The ENST00000720474.1(ENSG00000251511):​n.103+657G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,896 control chromosomes in the GnomAD database, including 19,787 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 0.51 (19787 hom., cov: 32)
• Consequence: ENSG00000251511 ENST00000720474.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 13 publications found

Genes affected

ENSG00000251511 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251511	ENST00000720474.1	n.103+657G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76917 AN: 151780 Hom.: 19772 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.507 AC: 76976 AN: 151896 Hom.: 19787 Cov.: 32 AF XY: 0.502 AC XY: 37292 AN XY: 74234

African (AFR) AF: 0.486 AC: 20138 AN: 41426

American (AMR) AF: 0.538 AC: 8197 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1465 AN: 3462

East Asian (EAS) AF: 0.507 AC: 2621 AN: 5166

South Asian (SAS) AF: 0.440 AC: 2117 AN: 4812

European-Finnish (FIN) AF: 0.454 AC: 4782 AN: 10536

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35834 AN: 67938

Other (OTH) AF: 0.546 AC: 1156 AN: 2116

Alfa AF: 0.488 Hom.: 5764

Bravo AF: 0.519

Asia WGS AF: 0.471 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	14
DANN	Benign	0.64
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1554472; hg19: chr4-157489906;