rs10517129

Variant names:

• chr4-27751739-C-T
• rs10517129
• ENST00000849360.1:n.171+6286C>T

Variant summary

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

The ENST00000849360.1(ENSG00000310375):​n.171+6286C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0599 in 152,212 control chromosomes in the GnomAD database, including 448 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 0.060 (448 hom., cov: 31)
• Consequence: ENSG00000310375 ENST00000849360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 0 publications found

Genes affected

ENSG00000310375 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310375	ENST00000849360.1	n.171+6286C>T		intron_variant	Intron 2 of 3
ENSG00000310375	ENST00000849361.1	n.364+6286C>T		intron_variant	Intron 3 of 5
ENSG00000310375	ENST00000849362.1	n.171+6286C>T		intron_variant	Intron 2 of 4
ENSG00000310375	ENST00000849363.1	n.362-3829C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9119 AN: 152094 Hom.: 449 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00539

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0333

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0599 AC: 9122 AN: 152212 Hom.: 448 Cov.: 31 AF XY: 0.0587 AC XY: 4370 AN XY: 74414

African (AFR) AF: 0.138 AC: 5716 AN: 41512

American (AMR) AF: 0.0224 AC: 343 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00540 AC: 26 AN: 4818

European-Finnish (FIN) AF: 0.0535 AC: 568 AN: 10610

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0333 AC: 2266 AN: 68020

Other (OTH) AF: 0.0440 AC: 93 AN: 2112

Alfa AF: 0.0421 Hom.: 230

Bravo AF: 0.0606

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.43
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs10517129; hg19: chr4-27753361;