1-175192463-G-T

Position:

• chr1-175192463-G-T

Variant summary

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

The NM_014656.3(KIAA0040):​c.-384+177C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,018 control chromosomes in the GnomAD database, including 5,487 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 0.24 (5487 hom., cov: 32)
• Consequence: KIAA0040 NM_014656.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

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=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA0040	NM_014656.3	c.-384+177C>A		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+177C>A		intron_variant		1	NM_014656.3	ENSP00000462172.1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36300 AN: 151900 Hom.: 5476 Cov.: 32

Gnomad AFR AF: 0.0709

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.239 AC: 36326 AN: 152018 Hom.: 5487 Cov.: 32 AF XY: 0.241 AC XY: 17883 AN XY: 74292

Gnomad4 AFR AF: 0.0709

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.285

Alfa AF: 0.204 Hom.: 909

Bravo AF: 0.255

Asia WGS AF: 0.315 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.1
DANN	Benign	0.85

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: rs2272785; hg19: chr1-175161599;