rs11156667

chr14-31367154-C-T

Variant summary

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

The NM_015473.4(HEATR5A):c.1962-2856G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,940 control chromosomes in the GnomAD database, including 15,469 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 0.45 (15469 hom., cov: 32)
• Consequence: HEATR5A NM_015473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

HEATR5A (HGNC:20276): (HEAT repeat containing 5A) Predicted to be involved in endocytosis; protein localization; and retrograde transport, endosome to Golgi. Predicted to be located in cytosol. Predicted to be active in endocytic vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HEATR5A	NM_015473.4	c.1962-2856G>A		intron_variant		ENST00000543095.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HEATR5A	ENST00000543095.7	c.1962-2856G>A		intron_variant		5	NM_015473.4	P1
HEATR5A	ENST00000538864.6	c.845-2856G>A		intron_variant		5
HEATR5A	ENST00000550366.5	c.889-2856G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67875 AN: 151822 Hom.: 15463 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.447 AC: 67909 AN: 151940 Hom.: 15469 Cov.: 32 AF XY: 0.443 AC XY: 32883 AN XY: 74254

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.469

Alfa AF: 0.494 Hom.: 8490

Bravo AF: 0.440

Asia WGS AF: 0.432 AC: 1495 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11156667; hg19: chr14-31836360;