rs77742018

chr8-95492244-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The NR_038201.1(CFAP418-AS1):n.281+59464A>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 0.023 in 152,318 control chromosomes in the GnomAD database, including 55 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 0.023 (55 hom., cov: 32)
• Consequence: CFAP418-AS1 NR_038201.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.023 (3502/152318) while in subpopulation NFE AF= 0.036 (2450/68016). AF 95% confidence interval is 0.0348. There are 55 homozygotes in gnomad4. There are 1667 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 55 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP418-AS1	NR_038201.1	n.281+59464A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP418-AS1	ENST00000655917.1	n.296+5750A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0230 AC: 3505 AN: 152200 Hom.: 55 Cov.: 32

Gnomad AFR AF: 0.00764

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0163

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00684

Gnomad FIN AF: 0.0327

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0360

Gnomad OTH AF: 0.0206

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

GnomAD4 genome AF: 0.0230 AC: 3502 AN: 152318 Hom.: 55 Cov.: 32 AF XY: 0.0224 AC XY: 1667 AN XY: 74480

Gnomad4 AFR AF: 0.00760

Gnomad4 AMR AF: 0.0163

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00684

Gnomad4 FIN AF: 0.0327

Gnomad4 NFE AF: 0.0360

Gnomad4 OTH AF: 0.0203

Alfa AF: 0.0319 Hom.: 8

Bravo AF: 0.0209

Asia WGS AF: 0.00231 AC: 8 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
Cadd	Benign	15
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77742018; hg19: chr8-96504472;