20-38213437-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4 BP6_Moderate BS2

The NM_001029864.2(KIAA1755):c.3208C>T(p.Arg1070Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000674 in 1,601,822 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0034 (1 hom., cov: 33)
  • Exomes 𝑓: 0.00038 (2 hom.)
• Consequence: KIAA1755 NM_001029864.2 stop_gained
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.148

Genes affected

KIAA1755 (HGNC:29372): (KIAA1755)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• PM4: Stoplost variant in NM_001029864.2 Downstream stopcodon found after 233 codons.
• BP6: Variant 20-38213437-G-A is Benign according to our data. Variant chr20-38213437-G-A is described in ClinVar as [Benign]. Clinvar id is 786678.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1755	NM_001029864.2	c.3208C>T	p.Arg1070Ter	stop_gained	14/14	ENST00000279024.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1755	ENST00000279024.9	c.3208C>T	p.Arg1070Ter	stop_gained	14/14	5	NM_001029864.2	P2
KIAA1755	ENST00000460881.5	n.1384C>T		non_coding_transcript_exon_variant	3/3	1
KIAA1755	ENST00000487506.1	n.1160C>T		non_coding_transcript_exon_variant	2/2	1
KIAA1755	ENST00000484362.1	n.1487C>T		non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes AF: 0.00340 AC: 518 AN: 152156 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00138

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000882

Gnomad OTH AF: 0.00191

GnomAD3 exomes AF: 0.000946 AC: 214 AN: 226120 Hom.: 3 AF XY: 0.000712 AC XY: 87 AN XY: 122218

Gnomad AFR exome AF: 0.0123

Gnomad AMR exome AF: 0.000779

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000589

Gnomad SAS exome AF: 0.000354

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000595

Gnomad OTH exome AF: 0.000179

GnomAD4 exome AF: 0.000383 AC: 555 AN: 1449548 Hom.: 2 Cov.: 60 AF XY: 0.000331 AC XY: 238 AN XY: 719872

Gnomad4 AFR exome AF: 0.00989

Gnomad4 AMR exome AF: 0.000771

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000255

Gnomad4 SAS exome AF: 0.000356

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000913

Gnomad4 OTH exome AF: 0.000919

GnomAD4 genome AF: 0.00344 AC: 524 AN: 152274 Hom.: 1 Cov.: 33 AF XY: 0.00325 AC XY: 242 AN XY: 74458

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.00137

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000882

Gnomad4 OTH AF: 0.00189

Alfa AF: 0.000639 Hom.: 1

Bravo AF: 0.00365

ESP6500AA AF: 0.00999 AC: 44

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.00111 AC: 134

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.034	T
BayesDel_noAF	Pathogenic	0.29
Cadd	Pathogenic	34
Dann	Uncertain	0.99
Eigen	Benign	0.17
Eigen_PC	Benign	-0.15
FATHMM_MKL	Benign	0.081	N
MutationTaster	Benign	1.0	D
Vest4		0.031
GERP RS		4.0

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: rs61748970; hg19: chr20-36841839;