rs7769940

Variant names:

• chr6-88240786-C-T
• rs7769940
• ENST00000648572.1:n.990+40028G>A

Variant summary

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

The ENST00000648572.1(ENSG00000234426):​n.990+40028G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 150,216 control chromosomes in the GnomAD database, including 9,456 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 0.31 (9456 hom., cov: 29)
• Consequence: ENSG00000234426 ENST00000648572.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 2 publications found

Genes affected

ENSG00000234426 (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 (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648572.1. 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
	ENSG00000234426	ENST00000648572.1		n.990+40028G>A		intron	N/A
	ENSG00000298549	ENST00000756364.1		n.311-4065C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 46809 AN: 150132 Hom.: 9431 Cov.: 29

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.312 AC: 46879 AN: 150216 Hom.: 9456 Cov.: 29 AF XY: 0.310 AC XY: 22757 AN XY: 73300

African (AFR) AF: 0.582 AC: 23758 AN: 40808

American (AMR) AF: 0.236 AC: 3546 AN: 15036

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 476 AN: 3458

East Asian (EAS) AF: 0.230 AC: 1185 AN: 5142

South Asian (SAS) AF: 0.239 AC: 1139 AN: 4768

European-Finnish (FIN) AF: 0.219 AC: 2191 AN: 9996

Middle Eastern (MID) AF: 0.221 AC: 64 AN: 290

European-Non Finnish (NFE) AF: 0.202 AC: 13709 AN: 67724

Other (OTH) AF: 0.288 AC: 603 AN: 2094

Alfa AF: 0.243 Hom.: 14546

Bravo AF: 0.326

Asia WGS AF: 0.292 AC: 1013 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	0.29
PhyloP100		-0.088

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: rs7769940;

hg19: chr6-88950505;