chr1-175187292-G-C

Position:

• chr1-175187292-G-C

Variant summary

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

The NM_014656.3(KIAA0040):​c.-384+5348C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,006 control chromosomes in the GnomAD database, including 18,763 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 0.49 (18763 hom., cov: 32)
• Consequence: KIAA0040 NM_014656.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.728

Genes affected

KIAA0040 (HGNC:28950): (KIAA0040) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

KIAA0040 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA0040	NM_014656.3	c.-384+5348C>G		intron_variant		ENST00000423313.6	NP_055471.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA0040	ENST00000423313.6	c.-384+5348C>G		intron_variant		1	NM_014656.3	ENSP00000462172.1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74409 AN: 151890 Hom.: 18770 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.490 AC: 74414 AN: 152006 Hom.: 18763 Cov.: 32 AF XY: 0.490 AC XY: 36402 AN XY: 74292

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.489

Alfa AF: 0.416 Hom.: 1306

Bravo AF: 0.465

Asia WGS AF: 0.464 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.4
DANN	Benign	0.62

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: rs3766685; hg19: chr1-175156428;