4-121978010-G-A

Variant names:

• chr4-121978010-G-A
• rs6838639
• ENST00000689735.3:n.132-1015G>A

Variant summary

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

The ENST00000689735.3(ENSG00000289342):​n.132-1015G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,034 control chromosomes in the GnomAD database, including 5,013 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 0.25 (5013 hom., cov: 31)
• Consequence: ENSG00000289342 ENST00000689735.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 18 publications found

Genes affected

ENSG00000289342 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000689735.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289342	ENST00000689735.3		n.132-1015G>A		intron	N/A
	ENSG00000289342	ENST00000691532.2		n.184-1015G>A		intron	N/A
	ENSG00000289342	ENST00000702483.2		n.108-5999G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37854 AN: 151916 Hom.: 5002 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.249 AC: 37892 AN: 152034 Hom.: 5013 Cov.: 31 AF XY: 0.253 AC XY: 18790 AN XY: 74310

African (AFR) AF: 0.193 AC: 8024 AN: 41472

American (AMR) AF: 0.388 AC: 5917 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3468

East Asian (EAS) AF: 0.320 AC: 1652 AN: 5164

South Asian (SAS) AF: 0.327 AC: 1571 AN: 4808

European-Finnish (FIN) AF: 0.218 AC: 2313 AN: 10588

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16717 AN: 67962

Other (OTH) AF: 0.256 AC: 540 AN: 2110

Alfa AF: 0.249 Hom.: 8486

Bravo AF: 0.261

Asia WGS AF: 0.337 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs6838639; hg19: chr4-122899165;