1-179742514-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000423879.5(ENSG00000243062):​n.361T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,926 control chromosomes in the GnomAD database, including 4,863 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 0.23 (4863 hom., cov: 32)
  • Exomes 𝑓: 0.21 (0 hom.)
• Consequence: ENSG00000243062 ENST00000423879.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC128071543	NR_138090.2	n.390T>G		non_coding_transcript_exon_variant	Exon 2 of 2
FAM163A	NM_001329713.2	c.-236+2T>G		splice_donor_variant, intron_variant	Intron 2 of 5		NP_001316642.1
FAM163A	NM_001329714.2	c.-258+2T>G		splice_donor_variant, intron_variant	Intron 2 of 6		NP_001316643.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243062	ENST00000423879.5	n.361T>G		non_coding_transcript_exon_variant	Exon 2 of 2	1
ENSG00000243062	ENST00000451471.1	n.245T>G		non_coding_transcript_exon_variant	Exon 2 of 2	3
ENSG00000243062	ENST00000669730.2	n.461T>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35447 AN: 151766 Hom.: 4865 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.263

GnomAD4 exome AF: 0.214 AC: 9 AN: 42 Hom.: 0 Cov.: 0 AF XY: 0.233 AC XY: 7 AN XY: 30

African (AFR) AF: 0.00 AC: 0 AN: 2

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) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.235 AC: 8 AN: 34

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.233 AC: 35459 AN: 151884 Hom.: 4863 Cov.: 32 AF XY: 0.238 AC XY: 17697 AN XY: 74248

African (AFR) AF: 0.177 AC: 7322 AN: 41392

American (AMR) AF: 0.350 AC: 5342 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 876 AN: 3468

East Asian (EAS) AF: 0.629 AC: 3234 AN: 5142

South Asian (SAS) AF: 0.272 AC: 1311 AN: 4822

European-Finnish (FIN) AF: 0.176 AC: 1855 AN: 10552

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14810 AN: 67932

Other (OTH) AF: 0.260 AC: 548 AN: 2106

Alfa AF: 0.224 Hom.: 11302

Bravo AF: 0.250

Asia WGS AF: 0.393 AC: 1364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.9
DANN	Benign	0.80
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1052447; hg19: chr1-179711649;