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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641778.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAF1-AS1	ENST00000641778.2		n.916T>C		non_coding_transcript_exon	Exon 3 of 3
	FAF1-AS1	ENST00000686764.2		n.866T>C		non_coding_transcript_exon	Exon 3 of 3
	FAF1-AS1	ENST00000754307.1		n.1151T>C		non_coding_transcript_exon	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 v4.9

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;