6-30465834-A-G

Variant names:

• chr6-30465834-A-G
• rs2524172
• ENST00000765496.1:n.842T>C

Variant summary

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

The ENST00000765496.1(ENSG00000288805):​n.842T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,176 control chromosomes in the GnomAD database, including 58,997 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 0.88 (58997 hom., cov: 31)
• Consequence: ENSG00000288805 ENST00000765496.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 23 publications found

Genes affected

ENSG00000288805 (HGNC:59165):

ENSG00000299674 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765496.1. 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
	ENSG00000288805	ENST00000765496.1		n.842T>C		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000288805	ENST00000765497.1		n.763T>C		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000299674	ENST00000765553.1		n.738A>G		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133768 AN: 152058 Hom.: 58944 Cov.: 31

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.880 AC: 133878 AN: 152176 Hom.: 58997 Cov.: 31 AF XY: 0.881 AC XY: 65564 AN XY: 74394

African (AFR) AF: 0.896 AC: 37178 AN: 41496

American (AMR) AF: 0.879 AC: 13446 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3200 AN: 3472

East Asian (EAS) AF: 0.990 AC: 5126 AN: 5178

South Asian (SAS) AF: 0.951 AC: 4580 AN: 4816

European-Finnish (FIN) AF: 0.895 AC: 9481 AN: 10596

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57900 AN: 68006

Other (OTH) AF: 0.879 AC: 1857 AN: 2112

Alfa AF: 0.867 Hom.: 213312

Bravo AF: 0.880

Asia WGS AF: 0.963 AC: 3351 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	2.8
DANN	Benign	0.46
PhyloP100		-0.037

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: rs2524172;

hg19: chr6-30433611;