chr1-179742514-T-C

Variant names:

• chr1-179742514-T-C
• rs1052447
• ENST00000423879.5:n.361T>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001329713.2(FAM163A):​c.-236+2T>C variant causes a splice donor, intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FAM163A NM_001329713.2 splice_donor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

ENSG00000243062 (HGNC:):

FAM163A (HGNC:28274): (family with sequence similarity 163 member A) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM163A	NM_001329713.2	c.-236+2T>C		splice_donor_variant, intron_variant	Intron 2 of 5		NP_001316642.1
FAM163A	NM_001329714.2	c.-258+2T>C		splice_donor_variant, intron_variant	Intron 2 of 6		NP_001316643.1
FAM163A	NM_001329715.2	c.-114+2T>C		splice_donor_variant, intron_variant	Intron 2 of 4		NP_001316644.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243062	ENST00000423879.5	n.361T>C		non_coding_transcript_exon_variant	Exon 2 of 2	1
ENSG00000243062	ENST00000451471.1	n.245T>C		non_coding_transcript_exon_variant	Exon 2 of 2	3
ENSG00000243062	ENST00000669730.1	n.387T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.4
DANN	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1052447; hg19: chr1-179711649;