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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901007	XR_007058824.1	n.981C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;