rs7013599

Positions:

• chr8-95673067-A-G
• chr8-95673067-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038201.1(CFAP418-AS1):​n.315+62370A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,078 control chromosomes in the GnomAD database, including 14,093 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 0.42 (14093 hom., cov: 32)
• Consequence: CFAP418-AS1 NR_038201.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760

Genes affected

CFAP418-AS1 (HGNC:50444): (CFAP418 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP418-AS1	NR_038201.1	n.315+62370A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP418-AS1	ENST00000655917.1	n.330+62370A>G		intron_variant, non_coding_transcript_variant
CFAP418-AS1	ENST00000517437.1	n.178+62370A>G		intron_variant, non_coding_transcript_variant		3
CFAP418-AS1	ENST00000664790.1	n.34+62370A>G		intron_variant, non_coding_transcript_variant
CFAP418-AS1	ENST00000671532.1	n.257+62370A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64194 AN: 151960 Hom.: 14095 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.455

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.422 AC: 64217 AN: 152078 Hom.: 14093 Cov.: 32 AF XY: 0.420 AC XY: 31239 AN XY: 74348

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.450

Alfa AF: 0.478 Hom.: 30685

Bravo AF: 0.420

Asia WGS AF: 0.338 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.28
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7013599; hg19: chr8-96685295;