rs4816018

Variant names:

• chr20-7675967-A-C
• rs4816018
• ENST00000839999.1:n.397-6968T>G

Your query was ambiguous. Multiple possible variants found:

• chr20-7675967-A-C
• chr20-7675967-A-G
• chr20-7675967-A-T

Variant summary

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

The ENST00000839999.1(ENSG00000309276):​n.397-6968T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,006 control chromosomes in the GnomAD database, including 6,467 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 0.28 (6467 hom., cov: 31)
• Consequence: ENSG00000309276 ENST00000839999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 2 publications found

Genes affected

ENSG00000309276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839999.1. 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
	ENSG00000309276	ENST00000839999.1		n.397-6968T>G		intron	N/A
	ENSG00000309276	ENST00000840000.1		n.76-6968T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42836 AN: 151890 Hom.: 6460 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.282 AC: 42868 AN: 152006 Hom.: 6467 Cov.: 31 AF XY: 0.281 AC XY: 20894 AN XY: 74320

African (AFR) AF: 0.181 AC: 7515 AN: 41486

American (AMR) AF: 0.393 AC: 5986 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1164 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1300 AN: 5140

South Asian (SAS) AF: 0.280 AC: 1345 AN: 4812

European-Finnish (FIN) AF: 0.253 AC: 2677 AN: 10580

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21807 AN: 67964

Other (OTH) AF: 0.313 AC: 662 AN: 2114

Alfa AF: 0.313 Hom.: 7687

Bravo AF: 0.292

Asia WGS AF: 0.302 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.7
DANN	Benign	0.90
PhyloP100		0.13

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: rs4816018;

hg19: chr20-7656614;