chr2-177612386-G-A

Variant names:

• chr2-177612386-G-A
• rs13031008
• ENST00000357045.4:n.86-4915G>A

Variant summary

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

The ENST00000357045.4(IFT70A-AS1):​n.86-4915G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,024 control chromosomes in the GnomAD database, including 33,354 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 0.64 (33354 hom., cov: 32)
• Consequence: IFT70A-AS1 ENST00000357045.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 7 publications found

Genes affected

IFT70A-AS1 (HGNC:58181):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000357045.4. 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
	IFT70A-AS1	NR_198966.1		n.115-4915G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFT70A-AS1	ENST00000357045.4	TSL:4	n.86-4915G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97144 AN: 151906 Hom.: 33341 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.639 AC: 97179 AN: 152024 Hom.: 33354 Cov.: 32 AF XY: 0.644 AC XY: 47890 AN XY: 74306

African (AFR) AF: 0.369 AC: 15304 AN: 41426

American (AMR) AF: 0.756 AC: 11551 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2391 AN: 3468

East Asian (EAS) AF: 0.665 AC: 3427 AN: 5156

South Asian (SAS) AF: 0.658 AC: 3172 AN: 4824

European-Finnish (FIN) AF: 0.826 AC: 8746 AN: 10582

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50440 AN: 67982

Other (OTH) AF: 0.655 AC: 1384 AN: 2112

Alfa AF: 0.706 Hom.: 111548

Bravo AF: 0.623

Asia WGS AF: 0.666 AC: 2315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.38
PhyloP100		-0.50

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: rs13031008;

hg19: chr2-178477114;