rs1551894

Variant names:

• chr5-75274706-G-A
• rs1551894
• XR_007058824.1:n.981C>T

Variant summary

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

The XR_007058824.1(LOC124901007):​n.981C>T 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 0.199 in 152,016 control chromosomes in the GnomAD database, including 3,405 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 0.20 (3405 hom., cov: 32)
• Consequence: LOC124901007 XR_007058824.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869
• Publications: 9 publications found

Genes affected

LOC124901007 (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 (SAS) allele frequency at 95% confidence interval = 0.335 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: 0.199 AC: 30273 AN: 151898 Hom.: 3407 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.199 AC: 30265 AN: 152016 Hom.: 3405 Cov.: 32 AF XY: 0.206 AC XY: 15313 AN XY: 74284

African (AFR) AF: 0.0940 AC: 3902 AN: 41504

American (AMR) AF: 0.217 AC: 3309 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 955 AN: 3464

East Asian (EAS) AF: 0.311 AC: 1600 AN: 5144

South Asian (SAS) AF: 0.349 AC: 1681 AN: 4818

European-Finnish (FIN) AF: 0.302 AC: 3176 AN: 10532

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14935 AN: 67974

Other (OTH) AF: 0.177 AC: 374 AN: 2110

Alfa AF: 0.212 Hom.: 6067

Bravo AF: 0.182

Asia WGS AF: 0.296 AC: 1029 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	0.48
DANN	Benign	0.19
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs1551894; hg19: chr5-74570531;