rs7281948

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC107985488 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985488	XR_001755005.1	n.145T>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.952

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.861

Alfa AF: 0.801 Hom.: 5563

Bravo AF: 0.882

Asia WGS AF: 0.937 AC: 3260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7281948; hg19: chr21-32970928;