rs7769940

Positions:

• chr6-88240786-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648572.1(ENSG00000234426):​n.990+40028G>A variant causes a intron, non coding transcript 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: ENST00000648572.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648572.1	n.990+40028G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.288

Alfa AF: 0.217 Hom.: 6558

Bravo AF: 0.326

Asia WGS AF: 0.292 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7769940; hg19: chr6-88950505;