rs7552721

Variant names:

• chr1-116360624-C-T
• rs7552721
• ENST00000813531.1:n.187-83G>A

Variant summary

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

The ENST00000813531.1(ENSG00000287217):​n.187-83G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,054 control chromosomes in the GnomAD database, including 10,131 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 0.24 (10131 hom., cov: 32)
• Consequence: ENSG00000287217 ENST00000813531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 2 publications found

Genes affected

ENSG00000287217 (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 = 0.671 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813531.1. 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
	ENSG00000287217	ENST00000813531.1		n.187-83G>A		intron	N/A
	ENSG00000287217	ENST00000813532.1		n.187-83G>A		intron	N/A
	ENSG00000287217	ENST00000813534.1		n.187-83G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36865 AN: 151950 Hom.: 10096 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0600

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.243 AC: 36954 AN: 152054 Hom.: 10131 Cov.: 32 AF XY: 0.236 AC XY: 17569 AN XY: 74316

African (AFR) AF: 0.677 AC: 28085 AN: 41466

American (AMR) AF: 0.165 AC: 2524 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0870 AC: 302 AN: 3472

East Asian (EAS) AF: 0.110 AC: 569 AN: 5180

South Asian (SAS) AF: 0.107 AC: 515 AN: 4816

European-Finnish (FIN) AF: 0.0251 AC: 264 AN: 10526

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.0600 AC: 4080 AN: 67994

Other (OTH) AF: 0.184 AC: 387 AN: 2104

Alfa AF: 0.113 Hom.: 4417

Bravo AF: 0.273

Asia WGS AF: 0.138 AC: 481 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	0.14
DANN	Benign	0.65
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7552721; hg19: chr1-116903246;