NM_153816.6:c.2654-264_2654-262delTTT

Variant names:

• chr6-85508320-TAAA-T
• rs765165360
• NM_153816.6:c.2654-264_2654-262delTTT

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The NM_153816.6(SNX14):​c.2654-264_2654-262delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0134 in 841,644 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00020 (0 hom., cov: 31)
  • Exomes 𝑓: 0.015 (0 hom.)
• Consequence: SNX14 NM_153816.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.80

Genes affected

SNX14 (HGNC:14977): (sorting nexin 14) This gene encodes a member of the sorting nexin family. Members of this family have a phox (PX) phosphoinositide binding domain and are involved in intracellular trafficking. The encoded protein also contains a regulator of G protein signaling (RGS) domain. Regulator of G protein signaling family members are regulatory molecules that act as GTPase activating proteins for G alpha subunits of heterotrimeric G proteins. Alternate splicing results in transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]

ENSG00000271793 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000202 (20/98958) while in subpopulation NFE AF= 0.000281 (13/46258). AF 95% confidence interval is 0.000166. There are 0 homozygotes in gnomad4. There are 11 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX14	NM_153816.6	c.2654-264_2654-262delTTT		intron_variant	Intron 26 of 28	ENST00000314673.8	NP_722523.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX14	ENST00000314673.8	c.2654-264_2654-262delTTT		intron_variant	Intron 26 of 28	1	NM_153816.6	ENSP00000313121.3
ENSG00000271793	ENST00000682083.1	n.*2564-264_*2564-262delTTT		intron_variant	Intron 37 of 39			ENSP00000506859.1

Frequencies

GnomAD3 genomes AF: 0.000202 AC: 20 AN: 98980 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000736

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000219

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000422

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000281

Gnomad OTH AF: 0.000741

GnomAD4 exome AF: 0.0151 AC: 11220 AN: 742686 Hom.: 0 AF XY: 0.0151 AC XY: 5202 AN XY: 345108

Gnomad4 AFR exome AF: 0.0148

Gnomad4 AMR exome AF: 0.0283

Gnomad4 ASJ exome AF: 0.0178

Gnomad4 EAS exome AF: 0.0279

Gnomad4 SAS exome AF: 0.0158

Gnomad4 FIN exome AF: 0.0504

Gnomad4 NFE exome AF: 0.0149

Gnomad4 OTH exome AF: 0.0155

GnomAD4 genome AF: 0.000202 AC: 20 AN: 98958 Hom.: 0 Cov.: 31 AF XY: 0.000234 AC XY: 11 AN XY: 46964

Gnomad4 AFR AF: 0.0000735

Gnomad4 AMR AF: 0.000219

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000422

Gnomad4 NFE AF: 0.000281

Gnomad4 OTH AF: 0.000739

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs765165360; hg19: chr6-86218038;