rs16847872

Variant names:

• chr1-175169153-A-G
• rs16847872
• NM_014656.3:c.-309-2416T>C

Variant summary

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

The ENST00000423313.6(KIAA0040):​c.-309-2416T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,290 control chromosomes in the GnomAD database, including 1,394 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 0.12 (1394 hom., cov: 33)
• Consequence: KIAA0040 ENST00000423313.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660
• Publications: 4 publications found

Genes affected

KIAA0040 (HGNC:28950): (KIAA0040) Predicted to be integral component of membrane. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423313.6. 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
	KIAA0040	NM_014656.3	MANE Select	c.-309-2416T>C		intron	N/A	NP_055471.2
	KIAA0040	NM_001162893.2		c.-309-2416T>C		intron	N/A	NP_001156365.1
	KIAA0040	NM_001162894.2		c.-309-2416T>C		intron	N/A	NP_001156366.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0040	ENST00000423313.6	TSL:1 MANE Select	c.-309-2416T>C		intron	N/A	ENSP00000462172.1
	KIAA0040	ENST00000444639.5	TSL:1	c.-309-2416T>C		intron	N/A	ENSP00000463734.1
	KIAA0040	ENST00000545251.6	TSL:1	c.-309-2416T>C		intron	N/A	ENSP00000464040.1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17775 AN: 152172 Hom.: 1393 Cov.: 33

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.117 AC: 17773 AN: 152290 Hom.: 1394 Cov.: 33 AF XY: 0.120 AC XY: 8901 AN XY: 74466

African (AFR) AF: 0.0271 AC: 1127 AN: 41582

American (AMR) AF: 0.0926 AC: 1417 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1614 AN: 5176

South Asian (SAS) AF: 0.256 AC: 1236 AN: 4824

European-Finnish (FIN) AF: 0.157 AC: 1668 AN: 10606

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9826 AN: 68006

Other (OTH) AF: 0.126 AC: 266 AN: 2114

Alfa AF: 0.136 Hom.: 4415

Bravo AF: 0.107

Asia WGS AF: 0.249 AC: 867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.1
DANN	Benign	0.82
PhyloP100		0.66
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: rs16847872; hg19: chr1-175138289;