rs1278527

Variant names:

• chr1-50425295-T-C
• rs1278527
• ENST00000641778.2:n.916T>C

Variant summary

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

The ENST00000641778.2(FAF1-AS1):​n.916T>C 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 0.471 in 152,280 control chromosomes in the GnomAD database, including 17,808 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 0.47 (17791 hom., cov: 33)
  • Exomes 𝑓: 0.49 (17 hom.)
• Consequence: FAF1-AS1 ENST00000641778.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 9 publications found

Genes affected

FAF1-AS1 (HGNC:40228): (FAF1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAF1-AS1	ENST00000641778.2	n.916T>C		non_coding_transcript_exon_variant	Exon 3 of 3
FAF1-AS1	ENST00000686764.2	n.866T>C		non_coding_transcript_exon_variant	Exon 3 of 3
FAF1-AS1	ENST00000754307.1	n.1151T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71504 AN: 152022 Hom.: 17748 Cov.: 33

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.499

GnomAD4 exome AF: 0.486 AC: 68 AN: 140 Hom.: 17 Cov.: 0 AF XY: 0.455 AC XY: 51 AN XY: 112

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.417 AC: 5 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.492 AC: 58 AN: 118

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.471 AC: 71582 AN: 152140 Hom.: 17791 Cov.: 33 AF XY: 0.457 AC XY: 33991 AN XY: 74370

African (AFR) AF: 0.576 AC: 23910 AN: 41498

American (AMR) AF: 0.391 AC: 5976 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2074 AN: 3472

East Asian (EAS) AF: 0.172 AC: 887 AN: 5172

South Asian (SAS) AF: 0.365 AC: 1763 AN: 4824

European-Finnish (FIN) AF: 0.298 AC: 3159 AN: 10588

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32228 AN: 67980

Other (OTH) AF: 0.503 AC: 1065 AN: 2116

Alfa AF: 0.466 Hom.: 3415

Bravo AF: 0.482

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.46
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1278527; hg19: chr1-50890967;