rs17098912

chr14-99637992-G-Achr14-99637992-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001329411.2(HHIPL1):c.60+12885G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,166 control chromosomes in the GnomAD database, including 2,251 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 0.16 (2251 hom., cov: 32)
• Consequence: HHIPL1 NM_001329411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

Genes affected

HHIPL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HHIPL1	NM_001329411.2	c.60+12885G>A		intron_variant
HHIPL1	XM_006720277.4	c.30+13003G>A		intron_variant
HHIPL1	XM_011537236.3	c.60+12885G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23924 AN: 152048 Hom.: 2248 Cov.: 32

Gnomad AFR AF: 0.0598

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.157 AC: 23939 AN: 152166 Hom.: 2251 Cov.: 32 AF XY: 0.162 AC XY: 12047 AN XY: 74408

Gnomad4 AFR AF: 0.0596

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.159

Alfa AF: 0.172 Hom.: 2480

Bravo AF: 0.143

Asia WGS AF: 0.298 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.5
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17098912; hg19: chr14-100104329;