rs4869987

Variant names:

• chr6-151111235-A-C
• rs4869987
• ENST00000415477.1:n.576-22855T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-151111235-A-C
• chr6-151111235-A-G
• chr6-151111235-A-T

Variant summary

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

The ENST00000772725.1(ENSG00000223598):​n.311-22855T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,318 control chromosomes in the GnomAD database, including 22,159 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 0.54 (22159 hom., cov: 29)
• Consequence: ENSG00000223598 ENST00000772725.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 2 publications found

Genes affected

ENSG00000223598 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772725.1. 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
	ENSG00000223598	ENST00000415477.1	TSL:5	n.576-22855T>G		intron	N/A
	ENSG00000223598	ENST00000772725.1		n.311-22855T>G		intron	N/A
	ENSG00000223598	ENST00000772726.1		n.321-22855T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81205 AN: 151204 Hom.: 22138 Cov.: 29

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.537 AC: 81269 AN: 151318 Hom.: 22159 Cov.: 29 AF XY: 0.533 AC XY: 39399 AN XY: 73908

African (AFR) AF: 0.468 AC: 19281 AN: 41234

American (AMR) AF: 0.579 AC: 8785 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1736 AN: 3466

East Asian (EAS) AF: 0.318 AC: 1628 AN: 5114

South Asian (SAS) AF: 0.455 AC: 2179 AN: 4794

European-Finnish (FIN) AF: 0.575 AC: 5996 AN: 10430

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 39964 AN: 67800

Other (OTH) AF: 0.536 AC: 1122 AN: 2094

Alfa AF: 0.545 Hom.: 11152

Bravo AF: 0.537

Asia WGS AF: 0.383 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.44
PhyloP100		-1.9

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: rs4869987;

hg19: chr6-151432371;