rs754524

Variant names:

• chr2-21088669-T-G
• rs754524
• ENST00000821616.1:n.239+7685A>C

Variant summary

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

The ENST00000821616.1(ENSG00000287956):​n.239+7685A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,230 control chromosomes in the GnomAD database, including 3,476 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 0.19 (3476 hom., cov: 32)
• Consequence: ENSG00000287956 ENST00000821616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• Publications: 17 publications found

Genes affected

ENSG00000287956 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821616.1. 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
	ENSG00000287956	ENST00000821616.1		n.239+7685A>C		intron	N/A
	ENSG00000287956	ENST00000821617.1		n.261+7685A>C		intron	N/A
	ENSG00000287956	ENST00000821618.1		n.241+7685A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29422 AN: 152112 Hom.: 3474 Cov.: 32

Gnomad AFR AF: 0.0573

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.193 AC: 29430 AN: 152230 Hom.: 3476 Cov.: 32 AF XY: 0.192 AC XY: 14324 AN XY: 74440

African (AFR) AF: 0.0572 AC: 2376 AN: 41564

American (AMR) AF: 0.264 AC: 4026 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 605 AN: 3464

East Asian (EAS) AF: 0.124 AC: 642 AN: 5190

South Asian (SAS) AF: 0.128 AC: 619 AN: 4828

European-Finnish (FIN) AF: 0.245 AC: 2599 AN: 10590

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17852 AN: 68002

Other (OTH) AF: 0.178 AC: 376 AN: 2116

Alfa AF: 0.244 Hom.: 4479

Bravo AF: 0.190

Asia WGS AF: 0.132 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.51
PhyloP100		-0.77

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: rs754524;

hg19: chr2-21311541;