rs6945374

Variant names:

• chr7-101593554-A-C
• rs6945374
• ENST00000786892.1:n.168+8637T>G

Variant summary

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

The ENST00000786892.1(ENSG00000302449):​n.168+8637T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,994 control chromosomes in the GnomAD database, including 2,712 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 0.19 (2712 hom., cov: 31)
• Consequence: ENSG00000302449 ENST00000786892.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 3 publications found

Genes affected

ENSG00000302449 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786892.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302449	ENST00000786892.1		n.168+8637T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28754 AN: 151876 Hom.: 2703 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.189 AC: 28776 AN: 151994 Hom.: 2712 Cov.: 31 AF XY: 0.185 AC XY: 13776 AN XY: 74304

African (AFR) AF: 0.186 AC: 7702 AN: 41450

American (AMR) AF: 0.153 AC: 2334 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3468

East Asian (EAS) AF: 0.157 AC: 809 AN: 5164

South Asian (SAS) AF: 0.202 AC: 973 AN: 4814

European-Finnish (FIN) AF: 0.187 AC: 1973 AN: 10578

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

European-Non Finnish (NFE) AF: 0.204 AC: 13870 AN: 67938

Other (OTH) AF: 0.188 AC: 396 AN: 2108

Alfa AF: 0.192 Hom.: 360

Bravo AF: 0.189

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.82
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs6945374; hg19: chr7-101236834;