6-85508320-TAAAAAAAA-TAAAA

Variant names:

• chr6-85508320-TAAAA-T
• rs765165360
• NM_153816.6:c.2654-265_2654-262delTTTT

Variant summary

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

The NM_153816.6(SNX14):​c.2654-265_2654-262delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0021 in 862,350 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 0.000030 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0024 (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 amr. gnomad4_exome allele frequency = 0.00237 (1808/763358) while in subpopulation AMR AF= 0.0115 (14/1218). AF 95% confidence interval is 0.00695. There are 0 homozygotes in gnomad4_exome. There are 824 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX14	NM_153816.6	c.2654-265_2654-262delTTTT		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.2654-265_2654-262delTTTT		intron_variant	Intron 26 of 28	1	NM_153816.6	ENSP00000313121.3
ENSG00000271793	ENST00000682083.1	n.*2564-265_*2564-262delTTTT		intron_variant	Intron 37 of 39			ENSP00000506859.1

Frequencies

GnomAD3 genomes AF: 0.0000303 AC: 3 AN: 99014 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000109

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000432

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00237 AC: 1808 AN: 763358 Hom.: 0 AF XY: 0.00232 AC XY: 824 AN XY: 354634

Gnomad4 AFR exome AF: 0.00210

Gnomad4 AMR exome AF: 0.0115

Gnomad4 ASJ exome AF: 0.00450

Gnomad4 EAS exome AF: 0.00743

Gnomad4 SAS exome AF: 0.00284

Gnomad4 FIN exome AF: 0.0143

Gnomad4 NFE exome AF: 0.00226

Gnomad4 OTH exome AF: 0.00308

GnomAD4 genome AF: 0.0000303 AC: 3 AN: 98992 Hom.: 0 Cov.: 31 AF XY: 0.0000638 AC XY: 3 AN XY: 46986

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000109

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000432

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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;