rs6991742

chr8-95452158-T-Cchr8-95452158-T-G

Variant summary

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

The NR_038201.1(CFAP418-AS1):n.281+19378T>C 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 0.462 in 152,012 control chromosomes in the GnomAD database, including 17,402 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 0.46 (17402 hom., cov: 32)
• Consequence: CFAP418-AS1 NR_038201.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP418-AS1	NR_038201.1	n.281+19378T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP418-AS1	ENST00000655917.1	n.211+19378T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70175 AN: 151894 Hom.: 17365 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.462 AC: 70268 AN: 152012 Hom.: 17402 Cov.: 32 AF XY: 0.458 AC XY: 34032 AN XY: 74306

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.442

Alfa AF: 0.287 Hom.: 646

Bravo AF: 0.462

Asia WGS AF: 0.335 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6991742; hg19: chr8-96464386;