rs3737933

chr1-175157508-G-Achr1-175157508-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.*3206C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,244 control chromosomes in the GnomAD database, including 58,641 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 0.87 (58641 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: KIAA0040 NM_014656.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

Genes affected

KIAA0040 (HGNC:28950): (KIAA0040) 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0040	NM_014656.3	c.*3206C>T		3_prime_UTR_variant	4/4	ENST00000423313.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0040	ENST00000423313.6	c.*3206C>T		3_prime_UTR_variant	4/4	1	NM_014656.3	P1
KIAA0040	ENST00000444639.5	c.*3206C>T		3_prime_UTR_variant	4/4	1		P1
KIAA0040	ENST00000619513.1	c.*2661C>T		3_prime_UTR_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.874 AC: 133009 AN: 152126 Hom.: 58573 Cov.: 32

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.863

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.874 AC: 133134 AN: 152244 Hom.: 58641 Cov.: 32 AF XY: 0.874 AC XY: 65052 AN XY: 74432

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.864

Alfa AF: 0.838 Hom.: 41002

Bravo AF: 0.881

Asia WGS AF: 0.742 AC: 2580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.5
Dann	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3737933; hg19: chr1-175126644; COSMIC: COSV70594073; COSMIC: COSV70594073;