rs10138277

Variant names:

• chr14-31393927-T-A
• rs10138277
• NM_015473.4:c.772+125A>T

Your query was ambiguous. Multiple possible variants found:

• chr14-31393927-T-A
• chr14-31393927-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015473.4(HEATR5A):​c.772+125A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HEATR5A NM_015473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 5 publications found

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]

ENSG00000203546 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HEATR5A	NM_015473.4	c.772+125A>T		intron_variant	Intron 6 of 35	ENST00000543095.7	NP_056288.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HEATR5A	ENST00000543095.7	c.772+125A>T		intron_variant	Intron 6 of 35	5	NM_015473.4	ENSP00000437968.2
ENSG00000203546	ENST00000549185.5	n.*868+125A>T		intron_variant	Intron 8 of 24	2		ENSP00000446654.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 518416 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 269896

African (AFR) AF: 0.00 AC: 0 AN: 12520

American (AMR) AF: 0.00 AC: 0 AN: 14688

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13562

East Asian (EAS) AF: 0.00 AC: 0 AN: 27962

South Asian (SAS) AF: 0.00 AC: 0 AN: 41808

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26738

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2116

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 351438

Other (OTH) AF: 0.00 AC: 0 AN: 27584

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 8589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.42
DANN	Benign	0.22
PhyloP100		-1.1

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

Other links and lift over

dbSNP: rs10138277; hg19: chr14-31863133;