rs6991742

Variant names:

• chr8-95452158-T-C
• rs6991742
• ENST00000517437.2:n.233+19378T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-95452158-T-C
• chr8-95452158-T-G

Variant summary

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

The ENST00000517437.2(CFAP418-AS1):​n.233+19378T>C variant causes a intron 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 ENST00000517437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517437.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP418-AS1	NR_038201.1		n.281+19378T>C		intron	N/A
	CFAP418-AS1	NR_038202.1		n.210+19378T>C		intron	N/A
	CFAP418-AS1	NR_038203.1		n.126+150966T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP418-AS1	ENST00000517437.2	TSL:3	n.233+19378T>C		intron	N/A
	CFAP418-AS1	ENST00000521905.3	TSL:5	n.304+19378T>C		intron	N/A
	CFAP418-AS1	ENST00000655917.1		n.211+19378T>C		intron	N/A

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

African (AFR) AF: 0.646 AC: 26756 AN: 41428

American (AMR) AF: 0.376 AC: 5743 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1367 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1039 AN: 5178

South Asian (SAS) AF: 0.354 AC: 1704 AN: 4808

European-Finnish (FIN) AF: 0.415 AC: 4375 AN: 10552

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27944 AN: 67978

Other (OTH) AF: 0.442 AC: 934 AN: 2114

Alfa AF: 0.309 Hom.: 786

Bravo AF: 0.462

Asia WGS AF: 0.335 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.49
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6991742;

hg19: chr8-96464386;