rs2385165

Variant names:

• chr8-123110274-A-C
• rs2385165
• NM_145647.4:c.1436+654A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-123110274-A-C
• chr8-123110274-A-G
• chr8-123110274-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145647.4(TBC1D31):​c.1436+654A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,036 control chromosomes in the GnomAD database, including 5,658 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 0.27 (5658 hom., cov: 32)
• Consequence: TBC1D31 NM_145647.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 6 publications found

Genes affected

TBC1D31 (HGNC:30888): (TBC1 domain family member 31) Located in centrosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145647.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBC1D31	NM_145647.4	MANE Select	c.1436+654A>C		intron	N/A	NP_663622.2
	TBC1D31	NM_001363149.1		c.1406+654A>C		intron	N/A	NP_001350078.1
	TBC1D31	NM_001363150.1		c.1436+654A>C		intron	N/A	NP_001350079.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBC1D31	ENST00000287380.6	TSL:1 MANE Select	c.1436+654A>C		intron	N/A	ENSP00000287380.1
	TBC1D31	ENST00000327098.9	TSL:1	c.1436+654A>C		intron	N/A	ENSP00000312701.5
	TBC1D31	ENST00000522420.5	TSL:1	c.1121+654A>C		intron	N/A	ENSP00000429334.1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40939 AN: 151918 Hom.: 5649 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.269 AC: 40967 AN: 152036 Hom.: 5658 Cov.: 32 AF XY: 0.270 AC XY: 20092 AN XY: 74312

African (AFR) AF: 0.271 AC: 11241 AN: 41432

American (AMR) AF: 0.338 AC: 5164 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 879 AN: 3466

East Asian (EAS) AF: 0.213 AC: 1102 AN: 5168

South Asian (SAS) AF: 0.302 AC: 1456 AN: 4824

European-Finnish (FIN) AF: 0.243 AC: 2574 AN: 10572

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17699 AN: 67992

Other (OTH) AF: 0.262 AC: 554 AN: 2114

Alfa AF: 0.268 Hom.: 3144

Bravo AF: 0.276

Asia WGS AF: 0.282 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-0.55
Mutation Taster		=100/0	polymorphism (auto)

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: rs2385165; hg19: chr8-124122514;