4-18615905-C-G

Variant names:

• chr4-18615905-C-G
• rs7671285
• ENST00000652661.1:n.419-13195C>G

Variant summary

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

The ENST00000652661.1(ENSG00000286046):​n.419-13195C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0301 in 152,236 control chromosomes in the GnomAD database, including 70 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 0.030 (70 hom., cov: 32)
• Consequence: ENSG00000286046 ENST00000652661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876
• Publications: 1 publications found

Genes affected

ENSG00000286046 (HGNC:59078):

LOC105374510 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0507 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652661.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286046	ENST00000652661.1		n.419-13195C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0301 AC: 4582 AN: 152118 Hom.: 70 Cov.: 32

Gnomad AFR AF: 0.0265

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0237

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0566

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0301 AC: 4578 AN: 152236 Hom.: 70 Cov.: 32 AF XY: 0.0292 AC XY: 2176 AN XY: 74442

African (AFR) AF: 0.0264 AC: 1096 AN: 41542

American (AMR) AF: 0.0237 AC: 363 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0430 AC: 149 AN: 3466

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5170

South Asian (SAS) AF: 0.0562 AC: 271 AN: 4818

European-Finnish (FIN) AF: 0.0225 AC: 239 AN: 10604

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0346 AC: 2353 AN: 68012

Other (OTH) AF: 0.0350 AC: 74 AN: 2114

Alfa AF: 0.0141 Hom.: 4

Bravo AF: 0.0292

Asia WGS AF: 0.0210 AC: 74 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		-0.88

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: rs7671285;

hg19: chr4-18617528;