11-112084759-G-T

Variant names:

• chr11-112084759-G-T
• rs544184
• NM_018195.4:c.*1787G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018195.4(NKAPD1):​c.*1787G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency: Genomes: not found (cov: 26)
• Consequence: NKAPD1 NM_018195.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 11 publications found

Genes affected

NKAPD1 (HGNC:25569): (NKAP domain containing 1) Enables identical protein binding activity. [provided by Alliance of Genome Resources, Apr 2022]

TIMM8B (HGNC:11818): (translocase of inner mitochondrial membrane 8 homolog B) This gene encodes a member of a well-conserved family of proteins with similarity to yeast Tim mitochondrial import proteins. This gene is encoded by a nuclear gene and is transported into the intermembrane space of the mitochondrion. When formed into complexes, these proteins guide membrane-spanning proteins across the mitochondrial intermembrane space before they are added into the mitochondrial inner membrane. This gene is adjacent to succinate dehydrogenase, subunit D (SDHD), in which mutations have been found in affected members of families with hereditary paraganglioma.[provided by RefSeq, Aug 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018195.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAPD1	NM_018195.4	MANE Select	c.*1787G>T		3_prime_UTR	Exon 6 of 6	NP_060665.3
	NKAPD1	NM_001082969.2		c.*1787G>T		3_prime_UTR	Exon 6 of 6	NP_001076438.1	Q6ZUT1-2
	NKAPD1	NM_001082970.2		c.*1787G>T		3_prime_UTR	Exon 6 of 6	NP_001076439.1	Q6ZUT1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAPD1	ENST00000393047.8	TSL:1 MANE Select	c.*1787G>T		3_prime_UTR	Exon 6 of 6	ENSP00000376767.3	Q6ZUT1-2
	NKAPD1	ENST00000968797.1		c.*1787G>T		3_prime_UTR	Exon 6 of 6	ENSP00000638856.1
	NKAPD1	ENST00000862992.1		c.*1787G>T		3_prime_UTR	Exon 6 of 6	ENSP00000533051.1

Frequencies

GnomAD3 genomes Cov.: 26

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 26

Alfa AF: 0.00 Hom.: 9904

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.56
PhyloP100		1.1

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

Other links and lift over

dbSNP: rs544184; hg19: chr11-111955483;