NM_014656.3:c.*3206C>T

Variant names:

• chr1-175157508-G-A
• rs3737933
• NM_014656.3:c.*3206C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.86).
• 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 rank	MANE	Protein	UniProt
KIAA0040	NM_014656.3	c.*3206C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000423313.6	NP_055471.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA0040	ENST00000423313.6	c.*3206C>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_014656.3	ENSP00000462172.1
KIAA0040	ENST00000444639.5	c.*3206C>T		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000463734.1
KIAA0040	ENST00000619513.1	c.*2661C>T		3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000478803.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.969 AC: 40283 AN: 41554

American (AMR) AF: 0.894 AC: 13689 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2895 AN: 3472

East Asian (EAS) AF: 0.697 AC: 3601 AN: 5170

South Asian (SAS) AF: 0.725 AC: 3488 AN: 4812

European-Finnish (FIN) AF: 0.876 AC: 9281 AN: 10590

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 57026 AN: 68018

Other (OTH) AF: 0.864 AC: 1824 AN: 2112

Alfa AF: 0.857 Hom.: 78387

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
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3737933; hg19: chr1-175126644; COSMIC: COSV70594073; COSMIC: COSV70594073;