rs10172929

Variant names:

• chr2-164192196-T-G
• rs10172929
• ENST00000429636.1:n.196+58524A>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000429636.1(ENSG00000237844):​n.196+58524A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.073 in 152,144 control chromosomes in the GnomAD database, including 554 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 0.073 (554 hom., cov: 32)
• Consequence: ENSG00000237844 ENST00000429636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

Genes affected

ENSG00000237844 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 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
ENSG00000237844	ENST00000429636.1	n.196+58524A>C		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0731 AC: 11108 AN: 152024 Hom.: 555 Cov.: 32

Gnomad AFR AF: 0.0206

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0708

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.0770

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0730 AC: 11103 AN: 152144 Hom.: 554 Cov.: 32 AF XY: 0.0689 AC XY: 5125 AN XY: 74346

Gnomad4 AFR AF: 0.0206

Gnomad4 AMR AF: 0.0707

Gnomad4 ASJ AF: 0.0418

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.0770

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0714

Alfa AF: 0.105 Hom.: 1292

Bravo AF: 0.0718

Asia WGS AF: 0.0130 AC: 44 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	22
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10172929; hg19: chr2-165048706;