4-18615905-C-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000286046 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374510	XR_001741601.2	n.823-13195C>G		intron_variant	Intron 2 of 6
LOC105374510	XR_001741602.2	n.91-13195C>G		intron_variant	Intron 1 of 5
LOC105374510	XR_925445.3	n.433-13195C>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286046	ENST00000652661.1	n.419-13195C>G		intron_variant	Intron 2 of 8

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

Gnomad4 AFR AF: 0.0264

Gnomad4 AMR AF: 0.0237

Gnomad4 ASJ AF: 0.0430

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0562

Gnomad4 FIN AF: 0.0225

Gnomad4 NFE AF: 0.0346

Gnomad4 OTH AF: 0.0350

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7671285; hg19: chr4-18617528;