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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905593	XR_007088659.1	n.579-7452T>G		intron_variant	Intron 1 of 2
LOC124905593	XR_007088660.1	n.579-7452T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287956	ENST00000821616.1	n.239+7685A>C		intron_variant	Intron 1 of 1
ENSG00000287956	ENST00000821617.1	n.261+7685A>C		intron_variant	Intron 1 of 2
ENSG00000287956	ENST00000821618.1	n.241+7685A>C		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs754524; hg19: chr2-21311541;