rs7121790

Variant names:

• chr11-45043414-G-A
• rs7121790
• ENST00000654627.2:n.501-281G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-45043414-G-A
• chr11-45043414-G-C

Variant summary

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

The ENST00000654627.2(ENSG00000287984):​n.501-281G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,238 control chromosomes in the GnomAD database, including 2,370 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 0.15 (2370 hom., cov: 33)
• Consequence: ENSG00000287984 ENST00000654627.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.839
• Publications: 0 publications found

Genes affected

ENSG00000287984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654627.2. 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
	ENSG00000287984	ENST00000654627.2		n.501-281G>A		intron	N/A
	ENSG00000294396	ENST00000723346.1		n.121+12521C>T		intron	N/A
	ENSG00000287984	ENST00000723452.1		n.500-274G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23287 AN: 152120 Hom.: 2372 Cov.: 33

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.153 AC: 23274 AN: 152238 Hom.: 2370 Cov.: 33 AF XY: 0.149 AC XY: 11114 AN XY: 74432

African (AFR) AF: 0.0437 AC: 1816 AN: 41584

American (AMR) AF: 0.142 AC: 2166 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5190

South Asian (SAS) AF: 0.0838 AC: 404 AN: 4822

European-Finnish (FIN) AF: 0.225 AC: 2382 AN: 10584

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15264 AN: 67976

Other (OTH) AF: 0.161 AC: 340 AN: 2110

Alfa AF: 0.197 Hom.: 10451

Bravo AF: 0.144

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.44
PhyloP100		0.84

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: rs7121790;

hg19: chr11-45064965;