rs6506640

Variant names:

• chr18-9099202-G-A
• rs6506640
• ENST00000827765.1:n.123+3202C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-9099202-G-A
• chr18-9099202-G-C
• chr18-9099202-G-T

Variant summary

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

The ENST00000827765.1(ENSG00000288939):​n.123+3202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,100 control chromosomes in the GnomAD database, including 51,221 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 0.82 (51221 hom., cov: 30)
• Consequence: ENSG00000288939 ENST00000827765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 3 publications found

Genes affected

ENSG00000288939 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827765.1. 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
	ENSG00000288939	ENST00000827765.1		n.123+3202C>T		intron	N/A
	ENSG00000288939	ENST00000827767.1		n.100+3202C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124586 AN: 151982 Hom.: 51177 Cov.: 30

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.820 AC: 124682 AN: 152100 Hom.: 51221 Cov.: 30 AF XY: 0.817 AC XY: 60707 AN XY: 74344

African (AFR) AF: 0.808 AC: 33528 AN: 41474

American (AMR) AF: 0.776 AC: 11854 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3165 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3810 AN: 5166

South Asian (SAS) AF: 0.865 AC: 4171 AN: 4824

European-Finnish (FIN) AF: 0.778 AC: 8224 AN: 10572

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57121 AN: 68008

Other (OTH) AF: 0.836 AC: 1765 AN: 2110

Alfa AF: 0.787 Hom.: 2628

Bravo AF: 0.818

Asia WGS AF: 0.755 AC: 2625 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	1.4
DANN	Benign	0.73
PhyloP100		-1.5

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: rs6506640;

hg19: chr18-9099200;