rs7156173

chr14-67452966-C-Achr14-67452966-C-G

Variant summary

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

The XR_007064213.1(LOC105370542):n.9019G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,128 control chromosomes in the GnomAD database, including 3,873 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 0.20 (3873 hom., cov: 32)
• Consequence: LOC105370542 XR_007064213.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

Genes affected

LOC105370542 (HGNC:):

TMEM229B (HGNC:20130): (transmembrane protein 229B) Predicted to act upstream of or within response to bacterium. Predicted to be integral component of membrane. [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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370542	XR_007064213.1	n.9019G>T		non_coding_transcript_exon_variant	3/3
GPHN	XM_047430879.1	c.1313-282229C>A		intron_variant
LOC105370542	XR_007064214.1	n.8425G>T		non_coding_transcript_exon_variant	3/3
LOC105370542	XR_943964.3	n.3196G>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM229B	ENST00000555638.5	c.*1132+1114G>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30319 AN: 152010 Hom.: 3866 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0872

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.200 AC: 30360 AN: 152128 Hom.: 3873 Cov.: 32 AF XY: 0.198 AC XY: 14746 AN XY: 74388

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0872

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.199

Alfa AF: 0.133 Hom.: 1663

Bravo AF: 0.214

Asia WGS AF: 0.201 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.12
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7156173; hg19: chr14-67919683;