rs6947787

Variant names:

• chr7-140263596-A-G
• rs6947787
• ENST00000825081.1:n.348-830T>C

Variant summary

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

The ENST00000825081.1(ENSG00000307329):​n.348-830T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,142 control chromosomes in the GnomAD database, including 3,037 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 0.17 (3037 hom., cov: 32)
• Consequence: ENSG00000307329 ENST00000825081.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 2 publications found

Genes affected

ENSG00000307329 (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 (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825081.1. 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
	ENSG00000307329	ENST00000825081.1		n.348-830T>C		intron	N/A
	ENSG00000307329	ENST00000825082.1		n.317+7063T>C		intron	N/A
	ENSG00000307329	ENST00000825083.1		n.317-830T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25066 AN: 152024 Hom.: 3029 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.0773

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.165 AC: 25105 AN: 152142 Hom.: 3037 Cov.: 32 AF XY: 0.162 AC XY: 12085 AN XY: 74400

African (AFR) AF: 0.351 AC: 14542 AN: 41472

American (AMR) AF: 0.0996 AC: 1522 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3470

East Asian (EAS) AF: 0.0771 AC: 399 AN: 5174

South Asian (SAS) AF: 0.113 AC: 544 AN: 4824

European-Finnish (FIN) AF: 0.117 AC: 1239 AN: 10606

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0899 AC: 6116 AN: 67998

Other (OTH) AF: 0.155 AC: 326 AN: 2110

Alfa AF: 0.115 Hom.: 1552

Bravo AF: 0.170

Asia WGS AF: 0.107 AC: 373 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	0.26
DANN	Benign	0.70
PhyloP100		-0.41

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: rs6947787;

hg19: chr7-139963396;