rs4697708

Variant names:

• chr4-10119565-T-C
• rs4697708
• ENST00000701208.2:n.*88T>C

Variant summary

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

The ENST00000701208.2(ENSG00000289865):​n.*88T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,112 control chromosomes in the GnomAD database, including 8,631 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 0.33 (8631 hom., cov: 33)
• Consequence: ENSG00000289865 ENST00000701208.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 7 publications found

Genes affected

ENSG00000289865 (HGNC:58731):

LOC124900666 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701208.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289865	ENST00000701208.2		n.*88T>C		downstream_gene	N/A
	ENSG00000289865	ENST00000818624.1		n.*86T>C		downstream_gene	N/A
	ENSG00000289865	ENST00000818625.1		n.*88T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49774 AN: 151994 Hom.: 8623 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.327 AC: 49798 AN: 152112 Hom.: 8631 Cov.: 33 AF XY: 0.328 AC XY: 24363 AN XY: 74356

African (AFR) AF: 0.215 AC: 8935 AN: 41500

American (AMR) AF: 0.355 AC: 5425 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1297 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1007 AN: 5180

South Asian (SAS) AF: 0.284 AC: 1366 AN: 4812

European-Finnish (FIN) AF: 0.395 AC: 4177 AN: 10574

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26532 AN: 67978

Other (OTH) AF: 0.342 AC: 723 AN: 2112

Alfa AF: 0.355 Hom.: 1731

Bravo AF: 0.317

Asia WGS AF: 0.242 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.56
DANN	Benign	0.55
PhyloP100		-2.0

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: rs4697708;

hg19: chr4-10121189;