chr6-31662176-A-T

Variant names:

• chr6-31662176-A-T
• rs7029
• NM_033177.4:c.*90T>A

Variant summary

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

The NM_033177.4(GPANK1):​c.*90T>A variant causes a 3 prime UTR 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GPANK1 NM_033177.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 37 publications found

Genes affected

GPANK1 (HGNC:13920): (G-patch domain and ankyrin repeats 1) This gene is located in a cluster of HLA-B-associated transcripts, which is included in the human major histocompatability complex III region. This gene encodes a protein which is thought to play a role in immunity. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Nov 2010]

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=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033177.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPANK1	NM_033177.4	MANE Select	c.*90T>A		3_prime_UTR	Exon 3 of 3	NP_149417.1
	GPANK1	NM_001199237.1		c.*90T>A		3_prime_UTR	Exon 4 of 4	NP_001186166.1
	GPANK1	NM_001199238.1		c.*90T>A		3_prime_UTR	Exon 4 of 4	NP_001186167.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPANK1	ENST00000375896.9	TSL:1 MANE Select	c.*90T>A		3_prime_UTR	Exon 3 of 3	ENSP00000365060.4
	GPANK1	ENST00000375893.6	TSL:5	c.*90T>A		3_prime_UTR	Exon 4 of 4	ENSP00000365057.2
	GPANK1	ENST00000375895.6	TSL:5	c.*90T>A		3_prime_UTR	Exon 4 of 4	ENSP00000365059.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 655586 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 338780

African (AFR) AF: 0.00 AC: 0 AN: 15986

American (AMR) AF: 0.00 AC: 0 AN: 23242

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14432

East Asian (EAS) AF: 0.00 AC: 0 AN: 32408

South Asian (SAS) AF: 0.00 AC: 0 AN: 48452

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47146

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3782

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 438126

Other (OTH) AF: 0.00 AC: 0 AN: 32012

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.73
PhyloP100		0.11

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: rs7029; hg19: chr6-31629953;