rs7281948

Variant names:

• chr21-31598615-A-C
• rs7281948
• XR_001755005.1:n.145T>G

Your query was ambiguous. Multiple possible variants found:

• chr21-31598615-A-C
• chr21-31598615-A-T

Variant summary

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

The XR_001755005.1(LOC107985488):​n.145T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,198 control chromosomes in the GnomAD database, including 58,262 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 0.87 (58262 hom., cov: 32)
• Consequence: LOC107985488 XR_001755005.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 3 publications found

Genes affected

LOC107985488 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132585 AN: 152080 Hom.: 58201 Cov.: 32

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.872 AC: 132702 AN: 152198 Hom.: 58262 Cov.: 32 AF XY: 0.873 AC XY: 64951 AN XY: 74394

African (AFR) AF: 0.952 AC: 39552 AN: 41544

American (AMR) AF: 0.898 AC: 13729 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3101 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5136 AN: 5160

South Asian (SAS) AF: 0.876 AC: 4226 AN: 4822

European-Finnish (FIN) AF: 0.817 AC: 8656 AN: 10590

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55414 AN: 68008

Other (OTH) AF: 0.861 AC: 1819 AN: 2112

Alfa AF: 0.807 Hom.: 5907

Bravo AF: 0.882

Asia WGS AF: 0.937 AC: 3260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.74
PhyloP100		-0.098

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: rs7281948;

hg19: chr21-32970928;