XR_007088659.1:n.578+972G>A

Variant names:

• chr2-21072103-G-A
• rs541041
• ENST00000821616.1:n.240-22322C>T

Variant summary

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

The XR_007088659.1(LOC124905593):​n.578+972G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,890 control chromosomes in the GnomAD database, including 41,451 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 0.72 (41451 hom., cov: 31)
• Consequence: LOC124905593 XR_007088659.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 39 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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.240-22322C>T		intron	N/A
	ENSG00000287956	ENST00000821617.1		n.262-13992C>T		intron	N/A
	ENSG00000287956	ENST00000821618.1		n.242-4462C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109046 AN: 151772 Hom.: 41443 Cov.: 31

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.718 AC: 109094 AN: 151890 Hom.: 41451 Cov.: 31 AF XY: 0.724 AC XY: 53775 AN XY: 74232

African (AFR) AF: 0.446 AC: 18477 AN: 41412

American (AMR) AF: 0.797 AC: 12175 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2423 AN: 3468

East Asian (EAS) AF: 0.994 AC: 5150 AN: 5182

South Asian (SAS) AF: 0.864 AC: 4165 AN: 4818

European-Finnish (FIN) AF: 0.817 AC: 8562 AN: 10478

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55542 AN: 67948

Other (OTH) AF: 0.727 AC: 1534 AN: 2110

Alfa AF: 0.794 Hom.: 216899

Bravo AF: 0.704

Asia WGS AF: 0.906 AC: 3146 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.044
DANN	Benign	0.42
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs541041; hg19: chr2-21294975;