chr1-175160810-C-T

Position:

• chr1-175160810-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_014656.3(KIAA0040):​c.204G>A​(p.Lys68Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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 0.61 (13995 hom., cov: 25)
  • Exomes 𝑓: 0.56 (89855 hom.)
  • Failed GnomAD Quality Control
• Consequence: KIAA0040 NM_014656.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514

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 Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BP7: Synonymous conserved (PhyloP=0.514 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA0040	NM_014656.3	c.204G>A	p.Lys68Lys	synonymous_variant	4/4	ENST00000423313.6	NP_055471.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA0040	ENST00000423313.6	c.204G>A	p.Lys68Lys	synonymous_variant	4/4	1	NM_014656.3	ENSP00000462172.1
KIAA0040	ENST00000444639.5	c.204G>A	p.Lys68Lys	synonymous_variant	4/4	1		ENSP00000463734.1
KIAA0040	ENST00000545251.6	c.204G>A	p.Lys68Lys	synonymous_variant	3/3	1		ENSP00000464040.1
KIAA0040	ENST00000619513.1	c.-180G>A		5_prime_UTR_variant	2/2	2		ENSP00000478803.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 64063 AN: 105202 Hom.: 13961 Cov.: 25 FAILED QC

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.624

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.556 AC: 509008 AN: 916132 Hom.: 89855 Cov.: 40 AF XY: 0.556 AC XY: 252241 AN XY: 453948

Gnomad4 AFR exome AF: 0.620

Gnomad4 AMR exome AF: 0.710

Gnomad4 ASJ exome AF: 0.638

Gnomad4 EAS exome AF: 0.589

Gnomad4 SAS exome AF: 0.562

Gnomad4 FIN exome AF: 0.569

Gnomad4 NFE exome AF: 0.541

Gnomad4 OTH exome AF: 0.566

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.609 AC: 64154 AN: 105318 Hom.: 13995 Cov.: 25 AF XY: 0.610 AC XY: 31565 AN XY: 51760

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.624

Alfa AF: 0.258 Hom.: 449

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	1.6
DANN	Benign	0.67

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: rs2072035; hg19: chr1-175129946; COSMIC: COSV70593739; COSMIC: COSV70593739;