rs10517472

Variant names:

• chr4-38285712-C-T
• rs10517472
• ENST00000757707.1:n.208-1449C>T

Variant summary

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

The ENST00000757707.1(ENSG00000251642):​n.208-1449C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,024 control chromosomes in the GnomAD database, including 7,818 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 0.31 (7818 hom., cov: 32)
• Consequence: ENSG00000251642 ENST00000757707.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 4 publications found

Genes affected

ENSG00000251642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374409	NR_188372.1	n.205-1449C>T		intron_variant	Intron 2 of 2
LOC105374409	NR_188373.1	n.109-1449C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251642	ENST00000757707.1	n.208-1449C>T		intron_variant	Intron 2 of 2
ENSG00000251642	ENST00000757708.1	n.367-1449C>T		intron_variant	Intron 2 of 2
ENSG00000251642	ENST00000757709.1	n.109-1449C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 47004 AN: 151904 Hom.: 7821 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.309 AC: 47022 AN: 152024 Hom.: 7818 Cov.: 32 AF XY: 0.304 AC XY: 22589 AN XY: 74304

African (AFR) AF: 0.190 AC: 7860 AN: 41458

American (AMR) AF: 0.345 AC: 5278 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3470

East Asian (EAS) AF: 0.149 AC: 769 AN: 5178

South Asian (SAS) AF: 0.221 AC: 1062 AN: 4810

European-Finnish (FIN) AF: 0.342 AC: 3600 AN: 10540

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25958 AN: 67970

Other (OTH) AF: 0.328 AC: 693 AN: 2114

Alfa AF: 0.357 Hom.: 18738

Bravo AF: 0.306

Asia WGS AF: 0.201 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.72
DANN	Benign	0.45
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10517472; hg19: chr4-38287333;