rs17002253

Variant names:

• chr4-76850192-T-C
• rs17002253
• XM_047416557.1:c.190-410T>C

Variant summary

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

The XM_047416557.1(LOC124900866):​c.190-410T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 152,224 control chromosomes in the GnomAD database, including 880 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 0.082 (880 hom., cov: 32)
• Consequence: LOC124900866 XM_047416557.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 6 publications found

Genes affected

LOC124900866 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 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: 0.0816 AC: 12409 AN: 152106 Hom.: 873 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0606

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0322

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0817 AC: 12433 AN: 152224 Hom.: 880 Cov.: 32 AF XY: 0.0820 AC XY: 6104 AN XY: 74440

African (AFR) AF: 0.189 AC: 7840 AN: 41516

American (AMR) AF: 0.0362 AC: 554 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3472

East Asian (EAS) AF: 0.0780 AC: 404 AN: 5182

South Asian (SAS) AF: 0.121 AC: 585 AN: 4822

European-Finnish (FIN) AF: 0.0606 AC: 643 AN: 10612

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0322 AC: 2191 AN: 68002

Other (OTH) AF: 0.0630 AC: 133 AN: 2112

Alfa AF: 0.0451 Hom.: 1267

Bravo AF: 0.0840

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.78
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs17002253; hg19: chr4-77771345;